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Amber: How to Prepare Amber: How to Prepare Parameters for Parameters for Non-standardNon-standard
ResiduesResidues
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RequirementsRequirements
1. Amber Modules: xleap/tleap, antechamber, parmchk, Gaussian (not a part of Amber)
2. Molecule Editor
3. Text Editor
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Parameter Preparation Workflow Parameter Preparation Workflow Using GaussianUsing Gaussian
Structure
Xleap/tleap
Text Editor
ResidueStructure
prepin file
Lib File
Gaussian
Output withESP Info
Molecule Editor
antechamber
parmchk
frcmod file
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Molecular/Structure EditorsMolecular/Structure Editors
Freeware (not many)
• Xleap (very basic editor facilities)
• Sirius sirius.sdsc.edu/• JMolEditor
sf.anu.edu.au/~vvv900/cct/appl/jmoleditor/index.html
Commercial Software
• Sybyl, HyperChem, Spartan, GaussView, etc.
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Parameter DerivationParameter Derivation
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Parameter Derivation:Parameter Derivation: Partial ChargesPartial Charges
QM = ab initio, DFT, semi-empirical
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Parameter Derivation: Parameter Derivation: Van der Waals ParametersVan der Waals Parameters
It is the most difficult part…
1) Optimizing van der Waals parameters to reproduce the experimental or high-level Quantum Chemical data
Could be computationally expensive
2) Optimizing van der Waals parameters through the Monte Carlo or MD simulations to reproduce the experimental properties of bulk solvent (density, etc.).
For example, OPLS van der Waals parameters Could be computationally expensive
3) Reusing existing van der Waals parameters for similar atom types from the same or other force field
The simplest approach
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Parameter Derivation:Parameter Derivation: Bond and Angle InteractionsBond and Angle Interactions
req and θeq come either from experimental data (X-ray, neutron diffraction) or Quantum Chemical calculations (geometry optimization)
Kr and Kθ force constants are usually optimized to reproduce the vibration frequencies calculated using high-level Quantum Chemical methods.
Or (the simplest approach)
Kr and Kθ force constants could be derived from the existing bond/angle parameters for similar bond/angle types from the same or other force field
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Parameter Derivation:Parameter Derivation: Dihedral Angle InteractionsDihedral Angle Interactions
Vn, n, and γ are derived to reproduce the rotational profile from the high-level Quantum Chemical calculations.
J.Wang et al., Development and testing of a general amber force field, Journal of Computational Chemistry, 25 (2004), 1157
Or (the simplest approach)
Vn, n, and γ could be derived from the existing dihedral angle parameters for similar dihedral angle types from the same or other force field
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Parameter Preparation Workflow Parameter Preparation Workflow Using GaussianUsing Gaussian
Xleap/tleap
prepin file
Lib File
Output withESP Info
antechamber
parmchk
frcmod file
Description of residue(s)
Parameter modification file
DerivedParameters
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Appendix
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Inhibitor covalently bonded Inhibitor covalently bonded to the Ser-195 of a proteinto the Ser-195 of a protein
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SEP (Ser-195)
PPH