HeroMDAnalysis An Automagical tool for GROMACS based Molecular
Dynamics Simulation Analysis
HeroMDAnalysis Step by Step Installation Guide
Please read the instructions given to install the tool You may also visit the video tutorial
provided here httpswwwyoutubecomwatchv=GGOmwzGWaSk
A) Step by Step Installation Guide (For Linux Machine)
Step 1 The user should be running a linux operating system The program is successfully
tested on Ubuntu and BOSS linux system But practically the tool should work on any linux
environment
Step 2 The user should have GROMACS 20194 or higher installed on your linux machine
Please visit GROMACS website httpwwwgromacsorg to know how to install GROMACS
Step 3 The user should have Xmgrace installed on your linux system If you want install
Xmgrace on debian based systems like Ubuntu and BOSS linux You can do it using terminal
by the following command sudo apt-get install grace and to install Xmgrace for other
distributions you may visit this website httpplasma-gateweizmannacilGrace
Step 4 The new version of the tool requires SHC Shell Compiler installed Use the following
commands to install SHC Shell Compiler on your linux machine First sudo add-apt-
repository ppaneurobinppa and second sudo apt-get update and then sudo
apt-get install shc
Step 5 After obtaining a copy of program extract the zip file in the folder where xtc edr and
tpr files of Molecular Dynamic simulation are placed and using terminal type following two
commands First chmod +x launchsh and finally launchsh to launch the tool
B) Step by Step Installation Guide (For Windows Machine with Linux Subsystem)
Step 1 The user should be running a windows operating system The program is successfully
tested on Windows 10 Then use the following tutorial to install linux subsystem on windows
httpswindowsloopcominstall-linux-subsystem-windows-10
Step 2 Install Xming on the windows machine by downloading the setup file from this website
httpssourceforgenetprojectsxming Then launch Xming and allow network access when
prompted through firewall application
Step 3 Install Zip and Unzip on the linux subsystem using the following commands For Zip
sudo apt-get install zip and for Unzip sudo apt-get install unzip
Step 4 Install Zenity on the linux subsystem using the following commands First sudo apt-
get update -y and then sudo apt-get install -y zenity
Step 5 The user should have GROMACS 20194 or higher installed on the linux subsystem
Please visit GROMACS website httpwwwgromacsorg to know how to install GROMACS
Step 6 The user should have Xmgrace installed on your linux system Please install it by the
following command sudo apt-get install -y grace
Step 7 The new version of the tool requires SHC Shell Compiler installed Use the following
commands to install SHC Shell Compiler on your linux machine First sudo add-apt-
repository ppaneurobinppa and second sudo apt-get update and then sudo
apt-get install shc
Step 8 After obtaining a copy of program extract the zip file in the folder where xtc edr and
tpr files of Molecular Dynamic simulation are placed and using terminal type following two
commands First chmod +x launchsh and finally DISPLAY=0 launchsh to launch
the tool
User manual
Module 1
The Program launch screen shows the program version list of developers
information regarding the tool website httpsheromdanalysiswordpresscom to visit for
more information and the terms and conditions user has to agree and accept before using this
tool Press Accept button to proceed further
Then comes the User authentication screen to authenticate the login and usage of the
tool The credentials for this screen must be obtained by filling the registration form available
at the website httpsheromdanalysiswordpresscomcontact-us
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
The selection window requires user to choose the system of analysis The available
options are a) Protein-ligand Complex or b) Apoprotein The options differ in the format that
there are ligand parameters available in the list of Protein-ligand complex while these are
absent in Apoprotein The user has to select one option for analysis and press the Select button
Selection menus for available parameters
In common theses screens would display list of available option for single or multiple
entries User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Selection screen for Root-mean-square-deviation
The graph is plotted for RMSD value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSD value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSD For example in Calpha-PL the RMSD
will be calculated by overlapping the Calpha atoms over the series of frames of
trajectory file
B) RMSD-L Lig fit Prot and Prot fit Lig are some other RMSD terms involving the
selection of ligand atoms one way or the other for the calculation for RMSD values for
the trajectory More information about these terms can be obtained from gromacs
website (wwwgromacsorg)
Selection screen for Root-mean-square-fluctuation
The graph is plotted for RMSF value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSF value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSF For example in Calpha-PL the RMSF
will be calculated by analyzing the fluctuation for Calpha atoms over the series of
frames of trajectory file
B) RMSF-L is RMSF term involving the selection of ligand atoms and then calculating
the fluctuation over the series of frames of the trajectory More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Radius of gyration
The graph is plotted for Rg value (nanometer) on y axis vs Time (picosecond) on x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will study
the compactness of the protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RoG For example in Calpha-PL the RoG will
be calculated by analyzing the distribution of Calpha atoms around the imaginary axis
of protein over the series of frames of trajectory file
B) RMSF-L is RoG term involving the selection of ligand atoms and then calculating the
compactness of ligand atoms over the series of frames of the trajectory More
information about these terms can be obtained from gromacs website
(wwwgromacsorg)
Selection screen for Solvent accessible surface area
The graph is plotted for area value (nanometer2) on y axis vs Time (picosecond) on x
axis
The list contains the options namely
A) Protein Residue or Atomic SASA to calculate solvent accessible surface area (y axis)
for each residue or atom in the ensemble (x axis) respectively The image generation is
only supported for the Protein-Residue SASA plot Please select this option to obtain a
plot SASA vs Residue number for protein
B) Ligand Fragment or Atomic SASA to calculate solvent accessible surface area (y
axis) for fragments or each atom in the ensemble (x axis) respectively The image
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Step 3 Install Zip and Unzip on the linux subsystem using the following commands For Zip
sudo apt-get install zip and for Unzip sudo apt-get install unzip
Step 4 Install Zenity on the linux subsystem using the following commands First sudo apt-
get update -y and then sudo apt-get install -y zenity
Step 5 The user should have GROMACS 20194 or higher installed on the linux subsystem
Please visit GROMACS website httpwwwgromacsorg to know how to install GROMACS
Step 6 The user should have Xmgrace installed on your linux system Please install it by the
following command sudo apt-get install -y grace
Step 7 The new version of the tool requires SHC Shell Compiler installed Use the following
commands to install SHC Shell Compiler on your linux machine First sudo add-apt-
repository ppaneurobinppa and second sudo apt-get update and then sudo
apt-get install shc
Step 8 After obtaining a copy of program extract the zip file in the folder where xtc edr and
tpr files of Molecular Dynamic simulation are placed and using terminal type following two
commands First chmod +x launchsh and finally DISPLAY=0 launchsh to launch
the tool
User manual
Module 1
The Program launch screen shows the program version list of developers
information regarding the tool website httpsheromdanalysiswordpresscom to visit for
more information and the terms and conditions user has to agree and accept before using this
tool Press Accept button to proceed further
Then comes the User authentication screen to authenticate the login and usage of the
tool The credentials for this screen must be obtained by filling the registration form available
at the website httpsheromdanalysiswordpresscomcontact-us
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
The selection window requires user to choose the system of analysis The available
options are a) Protein-ligand Complex or b) Apoprotein The options differ in the format that
there are ligand parameters available in the list of Protein-ligand complex while these are
absent in Apoprotein The user has to select one option for analysis and press the Select button
Selection menus for available parameters
In common theses screens would display list of available option for single or multiple
entries User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Selection screen for Root-mean-square-deviation
The graph is plotted for RMSD value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSD value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSD For example in Calpha-PL the RMSD
will be calculated by overlapping the Calpha atoms over the series of frames of
trajectory file
B) RMSD-L Lig fit Prot and Prot fit Lig are some other RMSD terms involving the
selection of ligand atoms one way or the other for the calculation for RMSD values for
the trajectory More information about these terms can be obtained from gromacs
website (wwwgromacsorg)
Selection screen for Root-mean-square-fluctuation
The graph is plotted for RMSF value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSF value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSF For example in Calpha-PL the RMSF
will be calculated by analyzing the fluctuation for Calpha atoms over the series of
frames of trajectory file
B) RMSF-L is RMSF term involving the selection of ligand atoms and then calculating
the fluctuation over the series of frames of the trajectory More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Radius of gyration
The graph is plotted for Rg value (nanometer) on y axis vs Time (picosecond) on x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will study
the compactness of the protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RoG For example in Calpha-PL the RoG will
be calculated by analyzing the distribution of Calpha atoms around the imaginary axis
of protein over the series of frames of trajectory file
B) RMSF-L is RoG term involving the selection of ligand atoms and then calculating the
compactness of ligand atoms over the series of frames of the trajectory More
information about these terms can be obtained from gromacs website
(wwwgromacsorg)
Selection screen for Solvent accessible surface area
The graph is plotted for area value (nanometer2) on y axis vs Time (picosecond) on x
axis
The list contains the options namely
A) Protein Residue or Atomic SASA to calculate solvent accessible surface area (y axis)
for each residue or atom in the ensemble (x axis) respectively The image generation is
only supported for the Protein-Residue SASA plot Please select this option to obtain a
plot SASA vs Residue number for protein
B) Ligand Fragment or Atomic SASA to calculate solvent accessible surface area (y
axis) for fragments or each atom in the ensemble (x axis) respectively The image
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Then comes the User authentication screen to authenticate the login and usage of the
tool The credentials for this screen must be obtained by filling the registration form available
at the website httpsheromdanalysiswordpresscomcontact-us
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
The selection window requires user to choose the system of analysis The available
options are a) Protein-ligand Complex or b) Apoprotein The options differ in the format that
there are ligand parameters available in the list of Protein-ligand complex while these are
absent in Apoprotein The user has to select one option for analysis and press the Select button
Selection menus for available parameters
In common theses screens would display list of available option for single or multiple
entries User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Selection screen for Root-mean-square-deviation
The graph is plotted for RMSD value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSD value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSD For example in Calpha-PL the RMSD
will be calculated by overlapping the Calpha atoms over the series of frames of
trajectory file
B) RMSD-L Lig fit Prot and Prot fit Lig are some other RMSD terms involving the
selection of ligand atoms one way or the other for the calculation for RMSD values for
the trajectory More information about these terms can be obtained from gromacs
website (wwwgromacsorg)
Selection screen for Root-mean-square-fluctuation
The graph is plotted for RMSF value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSF value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSF For example in Calpha-PL the RMSF
will be calculated by analyzing the fluctuation for Calpha atoms over the series of
frames of trajectory file
B) RMSF-L is RMSF term involving the selection of ligand atoms and then calculating
the fluctuation over the series of frames of the trajectory More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Radius of gyration
The graph is plotted for Rg value (nanometer) on y axis vs Time (picosecond) on x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will study
the compactness of the protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RoG For example in Calpha-PL the RoG will
be calculated by analyzing the distribution of Calpha atoms around the imaginary axis
of protein over the series of frames of trajectory file
B) RMSF-L is RoG term involving the selection of ligand atoms and then calculating the
compactness of ligand atoms over the series of frames of the trajectory More
information about these terms can be obtained from gromacs website
(wwwgromacsorg)
Selection screen for Solvent accessible surface area
The graph is plotted for area value (nanometer2) on y axis vs Time (picosecond) on x
axis
The list contains the options namely
A) Protein Residue or Atomic SASA to calculate solvent accessible surface area (y axis)
for each residue or atom in the ensemble (x axis) respectively The image generation is
only supported for the Protein-Residue SASA plot Please select this option to obtain a
plot SASA vs Residue number for protein
B) Ligand Fragment or Atomic SASA to calculate solvent accessible surface area (y
axis) for fragments or each atom in the ensemble (x axis) respectively The image
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
The selection window requires user to choose the system of analysis The available
options are a) Protein-ligand Complex or b) Apoprotein The options differ in the format that
there are ligand parameters available in the list of Protein-ligand complex while these are
absent in Apoprotein The user has to select one option for analysis and press the Select button
Selection menus for available parameters
In common theses screens would display list of available option for single or multiple
entries User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Selection screen for Root-mean-square-deviation
The graph is plotted for RMSD value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSD value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSD For example in Calpha-PL the RMSD
will be calculated by overlapping the Calpha atoms over the series of frames of
trajectory file
B) RMSD-L Lig fit Prot and Prot fit Lig are some other RMSD terms involving the
selection of ligand atoms one way or the other for the calculation for RMSD values for
the trajectory More information about these terms can be obtained from gromacs
website (wwwgromacsorg)
Selection screen for Root-mean-square-fluctuation
The graph is plotted for RMSF value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSF value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSF For example in Calpha-PL the RMSF
will be calculated by analyzing the fluctuation for Calpha atoms over the series of
frames of trajectory file
B) RMSF-L is RMSF term involving the selection of ligand atoms and then calculating
the fluctuation over the series of frames of the trajectory More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Radius of gyration
The graph is plotted for Rg value (nanometer) on y axis vs Time (picosecond) on x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will study
the compactness of the protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RoG For example in Calpha-PL the RoG will
be calculated by analyzing the distribution of Calpha atoms around the imaginary axis
of protein over the series of frames of trajectory file
B) RMSF-L is RoG term involving the selection of ligand atoms and then calculating the
compactness of ligand atoms over the series of frames of the trajectory More
information about these terms can be obtained from gromacs website
(wwwgromacsorg)
Selection screen for Solvent accessible surface area
The graph is plotted for area value (nanometer2) on y axis vs Time (picosecond) on x
axis
The list contains the options namely
A) Protein Residue or Atomic SASA to calculate solvent accessible surface area (y axis)
for each residue or atom in the ensemble (x axis) respectively The image generation is
only supported for the Protein-Residue SASA plot Please select this option to obtain a
plot SASA vs Residue number for protein
B) Ligand Fragment or Atomic SASA to calculate solvent accessible surface area (y
axis) for fragments or each atom in the ensemble (x axis) respectively The image
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
the trajectory More information about these terms can be obtained from gromacs
website (wwwgromacsorg)
Selection screen for Root-mean-square-fluctuation
The graph is plotted for RMSF value (nanometer) on y axis vs Time (nanosecond) on
x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will
calculate RMSF value for protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RMSF For example in Calpha-PL the RMSF
will be calculated by analyzing the fluctuation for Calpha atoms over the series of
frames of trajectory file
B) RMSF-L is RMSF term involving the selection of ligand atoms and then calculating
the fluctuation over the series of frames of the trajectory More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Radius of gyration
The graph is plotted for Rg value (nanometer) on y axis vs Time (picosecond) on x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will study
the compactness of the protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RoG For example in Calpha-PL the RoG will
be calculated by analyzing the distribution of Calpha atoms around the imaginary axis
of protein over the series of frames of trajectory file
B) RMSF-L is RoG term involving the selection of ligand atoms and then calculating the
compactness of ligand atoms over the series of frames of the trajectory More
information about these terms can be obtained from gromacs website
(wwwgromacsorg)
Selection screen for Solvent accessible surface area
The graph is plotted for area value (nanometer2) on y axis vs Time (picosecond) on x
axis
The list contains the options namely
A) Protein Residue or Atomic SASA to calculate solvent accessible surface area (y axis)
for each residue or atom in the ensemble (x axis) respectively The image generation is
only supported for the Protein-Residue SASA plot Please select this option to obtain a
plot SASA vs Residue number for protein
B) Ligand Fragment or Atomic SASA to calculate solvent accessible surface area (y
axis) for fragments or each atom in the ensemble (x axis) respectively The image
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Selection screen for Radius of gyration
The graph is plotted for Rg value (nanometer) on y axis vs Time (picosecond) on x axis
The list contains various options namely
A) Calpha-PL Backbone-PL Sidechain-PL and Protein-PL These options will study
the compactness of the protein-ligand complex (PL) and prefix terms denotes the
selection of atoms for the calculation of RoG For example in Calpha-PL the RoG will
be calculated by analyzing the distribution of Calpha atoms around the imaginary axis
of protein over the series of frames of trajectory file
B) RMSF-L is RoG term involving the selection of ligand atoms and then calculating the
compactness of ligand atoms over the series of frames of the trajectory More
information about these terms can be obtained from gromacs website
(wwwgromacsorg)
Selection screen for Solvent accessible surface area
The graph is plotted for area value (nanometer2) on y axis vs Time (picosecond) on x
axis
The list contains the options namely
A) Protein Residue or Atomic SASA to calculate solvent accessible surface area (y axis)
for each residue or atom in the ensemble (x axis) respectively The image generation is
only supported for the Protein-Residue SASA plot Please select this option to obtain a
plot SASA vs Residue number for protein
B) Ligand Fragment or Atomic SASA to calculate solvent accessible surface area (y
axis) for fragments or each atom in the ensemble (x axis) respectively The image
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
generation is only supported for the Ligand-Fragment SASA plot Please select this
option to obtain a plot SASA vs Fragment for ligand More information about these
terms can be obtained from gromacs website (wwwgromacsorg)
Selection screen for Free energy of solvation
The graph is plotted for change in Gibbrsquos free energy (kJmol) on y axis vs Time
(nanosecond) on x axis
The list contains the options namely
A) Protein Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for protein
B) Ligand Free energy of solvation This selection will calculate change in Gibbrsquos free
energy solvation term for ligand For more information about these terms please visit
gromacs website (wwwgromacsorg)
Selection screen for H-bond contact analysis
The graph is plotted for number of H-bond contacts on y axis vs Time (nanosecond) on
x axis
The list contains the options namely
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
A) Ligand-Protein H-bonds This option calculates the number of H-bond contacts
between ligand and protein for the complete duration of simulation
B) Intra-Protein H-bonds This option calculates the number of H-bond contacts
between among protein residues for the complete duration of simulation
C) Protein-Water H-bonds This option calculates the number of H-bond contacts
between protein and water molecules for the complete duration of simulation
Selection screen for H-bond contact analysis of various thermodynamic parameters
The list contains the options namely
A) Temperature The graphs is plotted between temperature (kelvin) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
B) Pressure The graphs is plotted between pressure (bar) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
C) Potential The graphs is plotted between potential (kJmol-1e-1) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
D) Density The graphs is plotted between density (kgm3) on y axis vs time (picosecond)
on x axis for complete duration of simulation trajectory
E) Total Energy The graphs is plotted between total energy (kJmol) on y axis vs time
(picosecond) on x axis for complete duration of simulation trajectory
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Selection screen for H-bond contact analysis of Principle component analysis
The raw data for these parameters is analysed and extracted The image processing for
these paramters is not done However the raw data obtained can be used and subjected to
Xmgrace and plots can be generated manually
The list contains the options namely
A) Covariance analysis for Backbone and Calpha
B) AnaEig analysis for Backbone and Calpha
C) 1D Eigenvec analysis for Backbone and Calpha
D) 2D Eigenvec analysis for Backbone and Calpha
E) RMSF Eigenvec analysis for Backbone and Calpha
Analysis of Parameters
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
The dialog for launching of selected jobs Press OK button to proceed Allow the tool
to work in the background All the data will be generated automatically and will be organized
in folders This will appear with lot of things happening in the folder Please donrsquot interfere
with any file being generated in this folder Other parallel tasks on the computer wonrsquot be
interfere
The progress bar displays progress level and text displays parameter name under current
progress Kindly wait for ldquoFinishedrdquo text to appear Until then donrsquot press any button
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
The job completion dialog which shows completed progress bar and ldquoFinishedrdquo
notified The tool now await confirmation by pressing OK button to proceed further
Plotting to High quality images
The selection window requires user to choose to plot images The available options are
a) Yes letrsquos plot data to HD quality images or b) No I donrsquot want it By selecting option a)
the raw data generated from the previous step would be plotted to HD quality images that can
be used for visualization and publication The option b) exits the tool here with the raw data
generated in previous step in an organized manner This data is always available for the user
and can be used to plot graphs using Xmgrace MS Excel or other plotting tools The user has
to select one option and press the OK button
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
If the user selected option b) the tools exits with the screen listing authors and other
information about the tool
If the user selects option a) then a notification for the beginning of plotting raw files to
HD quality image files appears And the user is prompted to provide some required information
on the subsequent steps
Prompt windows for required text to be placed on title of image files and axis information
required for plotting
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
1 PDB ID of the protein It is the 4-digit alpha-numeric code Please enter the required value
here For example 4PD4 Press OK button to proceed
2 Name of the ligand It is the name of the ligand that user wants to provide Please provide
name in the form of alphabets and numeric Kindly donrsquot use brackets and spaces in this
column For example C008234 Press OK button to proceed
3 Duration of the molecular dynamic simulation The unit for this value is in nanoseconds
For example for 100ns simulation the entry value is 100 Press OK button to proceed
Progress bar for plotting of selected parameters to image plots and text showing current
parameter under progress And notification for the user-interactive plotting of calpha_rmsd
plot Here user is asked to provide desired values in an entry box with Xmgrace window
opened in adjacent for reference
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
A screen with Xmgrace window on the left showing the calpha_rmsdxvg plot and entry
box on right awaiting user to enter the max value of y axis which can be 03 or other as required
by the user for the plot appearance
Similar screen with Xmgrace window on left showing calpha_rmsdxvg plot and entry
box on right awaiting user to enter the minor tick value of y axis which can be 005 or other as
required by the user for the appearance
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
A notification for the user-interactive plotting of calpha_rmsf plot Here the user is
asked to provide desired values to be filled in an entry box with Xmgrace window opened in
adjacent for reference Press OK button to proceed further
A screen with Xmgrace window on left showing the calpha_rmsfxvg plot and entry
box on right awaiting user to enter the max value of x axis The user has to point at the right
end of curve using mouse to read numeric value shown in the bar under the menus bar at the
top For example in this case the value was found to be 998 Press OK button to proceed
further
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Similarly the entry box on right await user input for min value of x axis Again the
user has to point at left end of the curve using mouse cursor and read value shown in the bar
under the menus bar at the top For example in this plot the value was found to be 670 Press
OK button to proceed further
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Similarly the entry box on right await user input for minor tick value of x axis Here
the user can look at the x axis at bottom to decide a suitable tick value For example in this
plot the value 25 was found to be optimum Press OK button to proceed further
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work
A similar set of steps are required for plotting the ligand_rmsdxvg data as done for
calpha_rmsdxvg
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
A similar set of steps are required for plotting the ligand_rmsfxvg data as done for
calpha_rmsfxvg
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
The progress bar displays progress level and text displays parameter name under current
progress Please wait for the progression of the work The upcoming data doesnrsquot require user
interactive plotting instead it progress with automation
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Screen for the successful completion of the plotting task Press OK button to proceed
further
An exit screen display information regarding name of developers and tool after
successfully completing assigned analysis and plotting tasks Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Module 2
The Program launch screen shows the program version module version information
regarding the tool website httpsheromdanalysiswordpresscom to visit for more
information and the terms and conditions user has to agree and accept before using this tool
Press Accept button to proceed further [Note The terminal window in the background should
be kept in this case of module II because module II takes user input for various steps through
the terminal]
This is the dialog to remind the user for the availability of three files namely
md_0_10tpr md_0_10edr and md_0_10xtc or md_0_10_fitxtc in the present working
directory of the tool Also the files generated would be organized and saved in this directory
Press Proceed button
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Selection menus for available parameters
The screen display list of available option for selection of single or multiple entries In
common all these parameters require an index file The first option being ldquoMake indexndx
filerdquo User may tick specific or all options and press Select button to proceed further If no
option is desired then press Skip button
Analysis of Parameters
1 Making Indexndx file
The program notifies for the parameter under progress and the user have to use
the terminal to select different point(s) for creating index file
The format for specifying any coordinate should be as
1) For a complete molecule (for example protein) 1
2) For a residue of the protein (for example residue 864) 1 amp r 864
3) For a specific atom of the protein (for example atom 1788 of residue 850) 1 amp r
850 amp a 1788
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Likewise single or multiple entries can be created
After specifying various points the user may use the pipe function to merge different
entries created into one in case multiple points have been created For example here entries
22 and 23 are getting merged using 22 | 23 function
The terminal would display the groups have been merged and a new merged entry have
been created
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
After successful creation of the entries in index file for various parameters like for
computing distance (at least two points must be specified) for computing angle (at least three
points must be specified) The user can end with typing q and hitting enter
The next screen asks the user to supply the name to save the index file
Here the user may specify the name and hit OK button [Note It is always better to
save the index file with coordinate information so any confusion in future could be avoided]
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
2 Compute Distance
For computing distance the program notifies the user to select the index file in which
two points have been specified for which the distance has to be calculated
The file selection dialog for the index file for computing distance The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
The next screen asks the user to supply the name to save the distance plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so any confusion in future could be avoided]
Now the distance computation will begin the program asks the user to specify the
positional pairs using the terminal
After carefully selecting the specific entry the user may press ctrl + D to begin the
calculations The raw data and image plots are saved in respected directories
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
3 Compute Angle
For computing angle the program notifies the user to select the index file in which three
points have been specified for which the angle has to be calculated
The file selection dialog for the index file for computing angle The user here can select
the particular index file and hit OK button
The next screen asks the user to supply the name to save the angle plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the angle computation will begin the program asks the user to specify the entry
for the three-atom pair using the terminal
The raw data and image plots are saved in respected directories
4 Compute Dihedral (Ramachandran Plot)
This calculation is done automatically and no user input is required in this case The
raw data and image plots are saved in respected directories
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
5 Compute Dihedral (per residue)
For computing dihedral on per residue basis the program notifies the user to specify
the particular residue
The residue selection dialog for computing dihedral on per residue basis The format
for specifying any residue should be as
1) For a residue (for example residue type Glycine at residue number 700) GLY-700
The raw data and image plots are saved in respected directories
6 Cluster structures
For clustering structures the program notifies the user to select the group for least
square fit and RMSD calculations
Using the terminal the user may specify the group for least square fit and RMSD
calculations For example if the C-alpha atoms are to be selected the user have to type 3 and
press enter
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
7 Compute RMSD using indexndx
For computing RMSD using indexndx the program notifies the user to select the index
file in which three or more points have been specified for which the Root-Mean-Square-
Deviation has to be calculated
The file selection dialog for the index file for computing RMSD The user here can
select the particular index file and hit OK button
The next screen asks the user to supply the name to save the rmsd plot xvg file Then
the user may specify the name and hit OK button [Note It is always better to save the plot file
with its coordinate information so any confusion in future could be avoided]
Now the RMSD computation will begin the program asks the user to specify the index
group for least square fit using the terminal
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
8 Compute RMSF using indexndx
For computing RMSF using indexndx the program notifies the user to select the index file
with the specific points for which the Root-Mean-Square-Fluctuation has to be calculated
Now the RMSF computation will begin the program asks the user to specify the index
group for root-mean-square calculation
After carefully selecting the specific entry the user may press enter to begin the
calculations The raw data and image plots are saved in respected directories
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
9 Compute ROG using indexndx
For computing ROG using indexndx the program notifies the user to select the index
file with the specific points for which the radius of gyration has to be calculated The next
screen asks the user to supply the name to save the rog plot xvg file
Here the user may specify the name and hit OK button [Note It is always better to
save the plot file with its coordinate information so as to avoid any confusion in future]
Now the radius of gyration calculation will begin the program asks the user to specify
the entry using the terminal
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit
After successful completion of all the tasks An exit screen would display information
regarding module and tool Press OK to exit