Version .0 2FWREHU 20

TINKERSoftware Tools for Molecular Design

TINKER

Software Tools for Molecular Design Version 6.0

October 2011

Copyright 1990-2011 by Jay William Ponder All Rights Reserved

2 TINKER User's Guide 2

Copyright 1990-2011 by Jay William Ponder All Rights Reserved User's Guide Cover Illustration by Jay Nelson Courtesy of Prof. R. T. Paine, Univ. of New Mexico TINKER IS PROVIDED "AS IS" AND WITHOUT ANY WARRANTY EXPRESS OR IMPLIED. THE USER ASSUMES ALL RISKS OF USING THIS SOFTWARE. THERE IS NO CLAIM OF THE MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE. YOU MAY MAKE COPIES OF TINKER FOR YOUR OWN USE, AND MODIFY THOSE COPIES. YOU MAY NOT DISTRIBUTE ANY MODIFIED SOURCE CODE OR DOCUMENTATION TO USERS AT ANY SITE OTHER THAN YOUR OWN. PLEASE SIGN AND RETURN THE TINKER LICENSE AGREEMENT IF YOU MAKE USE OF THIS SOFTWARE. V6.0 10/11

3 TINKER User's Guide 3

TINKER

Software Tools for Molecular Design Version 6.0 October 2011

Table of Contents Page 1. Introduction to the Software 5 2. Installation on your Computer 7 3. Types of Input & Output Files 10 4. Potential Energy Programs 13 5. Additional Utility Programs & Scripts 19 6. Special Features & Methods 23 7. Use of the Keyword Control File 29 8. Force Field Parameter Sets 61 9. Descriptions of Source Routines 69 10. Descriptions of Global Variables 139 11. Index of Function & Subroutine Calls 167 12. Test Cases & Examples 196 13. Benchmark Results 198 14. Collaborators & Acknowledgments 202 15. References & Suggested Reading 204

4 "#$%&' ()*+,) -./0* 4

5 "#$%&' ()*+,) -./0* 5

12 #34+50.64/53 45 47* 8594:;+* 153 V7#5cTWCX#?$#((@b1%8123C +dTC W4$4%&5 e217)4%: 153 W05 ?&28:(1(4&5: 053#2 #1%) B#53&2[: ^54>A \( 72#:#5(C&02 5#? %&3# 4: ?24((#5 &5 B124&0: _450> 7$1(=&2':C 153 &%%1:4&51$$< (#:(#3 =&2 %&'71(4;4$4(< &5

6 "#$%&' ()*+,) -./0* 6

B124&0: &= ()# &()#2 '1%)45# 153 VW %&';451(4&5: $4:(#3 1;&B#A \( 72#:#5(C ?# 12# 45 ()# 72&%#:: &=%&5B#2(456 &02 724'12< 3#B#$&7'#5( #==&2(: =2&' ]&2(215PP (& 1 '&2# '&3#25 ]&2(215 341$#%(A \'1%)45#@(215:$1(#3 U B#2:4&5 &= *+,-./ 4: %022#5($< 1B14$1;$#C 153 1 )153@(215:$1(#3 &7(4'4K#3 UB#2:4&5 &= 1 72#B4&0: *+,-./ 2#$#1:# 4: 1B14$1;$# =&2 45:7#%(4&5A U&5B#2:4&5 (& U &2 Uff 4: 053#2%&5:43#21(4&5C ;0( 5&( ;#456 1%(4B#$< 702:0#3 1( ()4: (4'#A *)# ;1:4% 3#:465 &= ()# #5#26< =05%(4&5 #5645# 0:#3 ;< ()# *+,-./ :E FLGMH RLN@MMQG #'14$E 7&53#2i31:)#2A?0:($A#30

+5 1334(4&5C 15 +5(#25#( ?#; :4(# %&5(145456 15 &5$45# B#2:4&5 &= ()4: ^:#2[: e043#C ()# '&:( 2#%#5(34:(24;0(4&5 B#2:4&5 &= ()# =0$$ *+,-./ 71%816# 153 &()#2 0:#=0$ 45=&2'1(4&5 %15 ;# =&053 1(http://dasher.wustl.edu/tinkerC ()# X&'# b16# =&2 ()# *+,-./ T&$#%0$12 T&3#$456b1%816#A

7 "#$%&' ()*+,) -./0* 7

D2 #3)4;BB;4/53 53 E5.+ ?5C@.4*+ How to Obtain a Copy of TINKER *)# *+,-./ 71%816# 4: 34:(24;0(#3 &5 ()# +5(#25#( B41 #4()#2 ()# ?#; :4(# &2 ()# 15&57$&2#2A

G+*A./B4 "#$%&' &H*6.4;AB*) *)# *+,-./ 71%816# 4: 1$:& 1B14$1;$# 1: %&'72#::#3 ^54> (12 12%)4B#:C "453&?: K47 =4$#:C 153 1: 1%&'7$#(# :#( &= 05%&'72#::#3 :&02%# 153 31(1 =4$#:A d45124#: 12# 72&B43#3 =&2 '1%)45#: 2055456"453&?: R`aT.a,*aJSSSa`bC _450>C 153 \77$# T1% VW `A \$$ &= ()#:# #>#%0(1;$#: 12# 72#:#5( 45:(153123 %&'72#::#3 =&2'1(: 1: 4534B4301$ 72&621': &2 1: %&'7$#(# :#(: &= #>#%0(1;$#:A +( 4:#>7#%(#3 ()1( &()#2 ^54> 0:#2: 153 bU 0:#2: ?)& 5##3 :7#%41$$< %0:(&'4K#3 B#2:4&5:C ?4$$ ;04$3;45124#: =&2 ()#42 :7#%4=4% :@:(

8 "#$%&' ()*+,) -./0* 8

6PP ]&2(215 %&'74$#2 1B14$1;$# =2&' http://gcc.gnu.org/ 4: 1$:& %171;$# &= ;04$3456 *+,-./&5 _450> 153 &()#2 ^54>@;1:#3 '1%)45#:A *)# _450> #>#%0(1;$#: ?# 72&B43# 12# ;04$( ?4() ()# +5(#$]&2(215 =&2 _450> QAS %&'74$#2A *)# b&2($153 e2&07 Fbe+H 153 \;:&=( b2&]&2(215 %&'74$#2: )1B# 1$:&;##5 (#:(#3 053#2 _450>C ;&() &= ?)4%) 6#5#21(# #>#%0(1;$#: 2&06)$< %&'7121;$# 45 :7##3 (& ()#+5(#$ %&'74$#2A V5 _450>C ()# 6PP #>#%0(1;$#: (#53 (& #>)4;4( 3#6213#3 7#2=&2'15%# %&'712#3 ?4()#>#%0(1;$#: =2&' %&''#2%41$ %&'74$#2:A W&'# ;#5%)'128 2#:0$(: 12# 72&B43#3 45 1 $1(#2 :#%(4&5 &=()4: ^:#2[: e043# ]&2 ()# T1%45(&:) ?# 34:(24;0(# #>#%0(1;$#: ;04$( 053#2 \77$# VW ` GSAL ?4() ()#e,^ 6PP %&'74$#2A *+,-./ 1$:& ;04$3: &5 ()# T1%45(&:) 0:456 ()# \;:&=( b2&]&2(215 %&'74$#2A ]&2bU: 2055456 "453&?: R`a,*aJSSSa`bC ()# 34:(24;0(#3 *+,-./ #>#%0(1;$#: 12# ;04$( 053#2 ()# +5(#$]&2(215 =&2 "453&?: QAS %&'74$#2A \$(#251(4B# "453&?: %&'74$#2: :0%) 1: U&'71I c4:01$ ]&2(215C_1)##%0(1;$#:A *)# #>#%0(1;$#: %15 ;# 2#51'#3 153 '&B#3 (&?)#2#B#2 #%0(1;$#: 45B&$B#: 2#7$1%456 ()# sockets.f :&02%# =4$# ?4() :&%8#(:A%C 15345%$03#3 ()# &;D#%( =2&' ()# U %&3# 45 ()# *+,-./ &;D#%( $4;212#%0(1;$#: '0:( ;# $458#316145:( g1B1 $4;2124#: 45 1334(4&5 (& ()# 0:01$ 2#:&02%#:A W1'7$# compgui.make 153linkgui.make :%247(: 12# 72&B43#3 =&2 :

9 "#$%&' ()*+,) -./0* 9

1$:& )#$7 0: D0:(4=< =02()#2 3#B#$&7'#5( &= *+,-./A ")#5 5#? '&30$#: 153 %171;4$4(4#: ;#%&'#1B14$1;$#C 153 ?)#5 ()# 1$'&:( 45#B4(1;$# ;06: 12# 05%&B#2#3C ?# ?4$$ 1((#'7( (& 5&(4=< ()&:# ?)&)1B# 2#(025#3 1 $4%#5:# =&2'A ]451$$

10 "#$%&' ()*+,) -./0* 10

L2 "E@*) 59 #3@.4 M J.4@.4 >/B*) *)4: :#%(4&5 3#:%24;#: ()# ;1:4% =4$# (

11 "#$%&' ()*+,) -./0* 11

*)# .end =4$# (

12 "#$%&' ()*+,) -./0* 12

8NOGP&2QOJP *)# \/UX+c. 72&621' )1: ()# &7(4&5 &= %&5B#2(456 1 :#24#: &= .xyz %

13 "#$%&' ()*+,) -./0* 13

W2 G54*34/;B &3*+XE G+5X+;C) *)4: :#%(4&5 &= ()# '1501$ %&5(145: 1 ;24#= 3#:%247(4&5 &= #1%) &= ()# *+,-./ 7&(#5(41$ #5#261'7$#C ?# 0:# \_UX.Tk 45 1 '&$#%0$12'&3#$456 %&02:# $1;&21(&2< #>#2%4:# (& 7#2=&2' :0%) %$1::4% '0(1(4&5: 1: %)$&243# (& ;2&'43# 153#()15# (& '#()15&$ 45 ?1(#2A *)# 72#:#5( B#2:4&5 0:#: ()# 7#2(02;1(4&5 =&2'0$1 153 ?453&?456 ?4()15 #>7$4%4( '177456 &= 1(&': 45B&$B#3 45 ()# '0(1(4&5 FZZ\Td./[[@:(

14 "#$%&' ()*+,) -./0* 14

50';#2#3 %

15 "#$%&' ()*+,) -./0* 15

\ (205%1(#3 ,#?(&5 '454'4K1(4&5 '#()&3 ?)4%) 2#I042#: 7&(#5(41$ #5#26

16 "#$%&' ()*+,) -./0* 16

#5#26< 45(#2'#341(#: %15 ;# 0:#3 1: 4570( (& 1 ,#?(&5@;1:#3 &7(4'4K1(4&5 (& $&%1(# %&5=&2'1(4&51$(215:4(4&5 :(1(#:A G88 +'7$#'#5(: &02 B#2:4&5 &= 1 7&(#5(41$ :'&&()456 153 :#12%) 1$6&24()' =&2 ()# 6$&;1$ &7(4'4K1(4&5 &='&$#%0$12 %&5=&2'1(4&5A \5 454(41$ :(20%(02# 45 .xyz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

17 "#$%&' ()*+,) -./0* 17

8$#>>&' \ 72&621' ()1( 4'7$#'#5(: ()# W54==#2 6$&;1$ &7(4'4K1(4&5 1$6&24()' &= d0($#2 153 W$1'4581C 134:%2#(# B#2:4&5 &= e24#?158[: 6$&;1$ :#12%) (21D#%(&2< '#()&3A *)# 72&621' (18#: 15 4570( *+,-./.xyz %&&23451(#: =4$# 153 :)18#: 4( B46&2&0:$< B41 1 '&34=4#3 31%($< ()# :1'# 15:?#2 45 1$$ %1:#:C :45%# ()# 43#5(4%1$ 4534B4301$ 45(#21%(4&5: 12# %&'70(#3 ;< ;&()'#()&3:A *)# 3#=10$( 3&0;$# $&&7 '#()&3 4: =1:(#2 ?)#5 %0(&==: 12# 5&( 0:#3C &2 ?)#5 ()# %0(&==:7)#2# %&5(145: 1;&0( )1$= &2 '&2# &= ()# (&(1$ :

18 "#$%&' ()*+,) -./0* 18

*)4: 72&621' 4: :4'4$12 (& *+T./C &5$< 4( &7#21(#: &B#2 34)#321$ 156$#: B41 4570( &= 1 *+,-./ .int45(#251$ %&&23451(# =4$#A +5 ()# %022#5( B#2:4&5C ()# (&2:4&51$ X#::415 4: %&'70(#3 50'#24%1$$< =2&'()# 151$#" *)# `*\_]+* 72&621' 4: &= 0:# 45 ()# 10(&'1(#3 =4((456 &= 7&(#5(41$ 7121'#(#2: (& %2

19 "#$%&' ()*+,) -./0* 19

[2 N00/4/53;B (4/B/4E G+5X+;C) M 86+/@4) *)4: :#%(4&5 &= ()# '1501$ %&5(145: 1 ;24#= 3#:%247(4&5 &= #1%) &= ()# *+,-./ :(20%(02# '15470$1(4&5C6#&'#(24% %1$%0$1(4&5 153 10>4$412< 72&621':A \ 3#(14$#3 #>1'7$# :)&?456 )&? (& 205 #1%) 72&621'4: 45%$03#3 45 1 $1(#2 :#%(4&5A *)# 72&621': $4:(#3 ;#$&? 12# 1$$ 712( &= ()# '145C :077&2(#334:(24;0(4&5A \334(4&51$ :&02%# %&3# =&2 B124&0: 05:077&2(#3 72&621': %15 ;# =&053 45 ()# a&()#2342#%(&2< &= ()# *+,-./ 34:(24;0(4&5A N'?Y#Z& \ 72&621' =&2 %&5%1(#51(456 *+,-./ %(#5:4&5H &2 ?4() `T18#'&$ F()#42 =4$# =&2'1( ?4() .xmol #>(#5:4&5HA V5$< 1%(4B# 1(&': 12# ?24((#545(& ()# +5:46)(++ 153 `T18#'&$ &0(70( =4$#:C 1$$&?456 34:7$1< &= 712(41$ :(20%(02#:A *)# 72&621' %151$:& #>(21%( 4534B4301$ %

20 "#$%&' ()*+,) -./0* 20

16145:( 1 6#&'#(24% 2#:(2145(@&5$< 7&(#5(41$ 0:456 #4()#2 1 :#I0#5(41$ '454'4K1(4&5 72&(&%&$ &2:4'0$1(#3 155#1$456A IJ?(O&$" *)# YVU^T.,* 72&621' 4: 72&B43#3 1: 1 '454'1$ $4:(456 153 3&%0'#5(1(4&5 (&&$A +( &7#21(#: &5 ()#*+,-./ :&02%# %&3#C #4()#2 4534B4301$ =4$#: &2 ()# %&'7$#(# :&02%# $4:(456 72&30%#3 ;< ()# %&''153:%247( listing.makeC (& 6#5#21(# $4:(: &= 2&0(45#:C %&''&5 ;$&%8: &2 B1$43 8#

21 "#$%&' ()*+,) -./0* 21

G'J"$ \ 72&621' =&2 10(&'1(#3 ;04$3456 &= 7#7(43# 153 72&(#45 :(20%(02#:A ^7&5 45(#21%(4B# 4570( &= 151'45& 1%43 :#I0#5%# ?4() &7(4&51$ 7)4a7:4a&'#61a%)4 156$#:C Ya_ %)421$4(

22 "#$%&' ()*+,) -./0* 22

QRS&I#" \ 72&621' ()1( 7#2=&2': 153 &= 1 B124#(< &= '15470$1(4&5: &5 15 4570( *+,-./ A>C FGNH W&18 U022#5( T&$#%0$# 45 d&> &=W&$B#5(C FGOH \77#53 15&()#2 `kj =4$# (& U022#5( V5#A +5 '&:( %1:#:C '0$(47$< &7(4&5: %15 ;# 177$4#3:#I0#5(41$$< (& 15 4570( =4$#A \( ()# #53 &= ()# #34(456 72&%#::C 1 5#? B#2:4&5 &= ()# &246451$ .xyz =4$#4: ?24((#5 1: &0(70(A QRS#$" \ 72&621' =&2 %&5B#2(456 1 *+,-./ .xyz U12(#:415 %&&23451(# =&2'1((#3 =4$# 45(& 1 *+,-./ .int45(#251$ %&&23451(#: =&2'1((#3 =4$#A *)4: 72&621' %15 &7(4&51$$< 0:# 15 #>4:(456 45(#251$ %&&23451(#:=4$# 1: 1 (#'7$1(# =&2 ()# %&55#%(4B4(< 45=&2'1(4&5A QRSGIV \ 72&621' =&2 %&5B#2(456 1 *+,-./ .xyz U12(#:415 %&&23451(# =4$# 45(& 1 d2&&8)1B#5 b2&(#45 Y1(1d158 =4$# F1 bYd =4$#HA QRS8RVRP \ 72&621' (& %&5B#2( 1 *+,-./ .xyz U12(#:415 %&&23451(#: =4$# 45(& 1 */+bVW W

23 "#$%&' ()*+,) -./0* 23

]2 8@*6/;B >*;4.+*) M O*4750) *)4: :#%(4&5 %&5(145: :#B#21$ :)&2( 5&(#: ?4() =02()#2 45=&2'1(4&5 1;&0( *+,-./ '#()&3&$&6/B* Z*+)/53 $.CA*+) \$$ &= ()# 4570( 153 &0(70( =4$# (4:(456 1:'0$(47$# B#2:4&5: &= 1 ;1:# =4$# 51'#A ]&2 #>1'7$#C 4= ()# 72&621' `kj+,* 4: 205 &5 ()# 4570( =4$#molecule.xyzC ()# &0(70( 45(#251$ %&&23451(#: =4$# ?4$$ ;# ?24((#5 (& molecule.intA += 1 =4$#51'#3 molecule.int 4: 1$2#13< 72#:#5( 724&2 (& 2055456 `kj+,*C ()#5 ()# &0(70( ?4$$ ;# ?24((#545:(#13 (& ()# 5#>( 1B14$1;$# B#2:4&5C 45 ()4: %1:# (& molecule.int_2A +5 =1%( ()# &0(70( 4: 6#5#21$$