* Justin A. Lemkul <[EMAIL PROTECTED]> [2008-09-10 05:46:07 -0400]:
Morteza Khabiri wrote:
Dear justin,
I have made the itp file on a basis of chapter 5 of gromacs. Every things
seems fine. my itp file for opls is as follow:
"Seems fine" is your own evaluation, but if grompp is giving you errors
about an incorrect topology, then indeed it is not. Did grompp tell you a
line number that caused the error? My guess would be yes. If you want free
help for solving this, you have to make it easy. What was the line? What
is on that line?
-Justin
;
[ moleculetype ]
; Name nrexcl
DRG 3
[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 opls_185 1 DRG HAD 1 0.02734 1.0080
2 opls_182 1 DRG CAL 1 0.10638 12.0110
3 opls_185 1 DRG HAE 1 0.02734 1.0080
4 opls_180 1 DRG OAI 1 -0.36111 15.9994
5 opls_182 1 DRG CAK 1 0.10638 12.0110
6 opls_185 1 DRG HAB 2 0.02734 1.0080
7 opls_185 1 DRG HAG 2 0.02734 1.0080
8 opls_711 1 DRG CAM 2 0.00235 12.0110
9 opls_777 1 DRG HAF 3 0.00857 1.0080
10 opls_777 1 DRG HAH 3 0.00857 1.0080
11 opls_711 1 DRG CAJ 3 0.00235 12.0110
12 opls_777 1 DRG HAC 3 0.00857 1.0080
13 opls_777 1 DRG HAA 3 0.00857 1.0080
[ bonds ]
; ai aj fu c0, c1, ...
1 2 1 0.109 284512.0 0.109 284512.0 ; HAD CAL
2 3 1 0.109 284512.0 0.109 284512.0 ; CAL HAE
2 4 1 0.141 267776.0 0.141 267776.0 ; CAL HAI
2 11 1 0.152 217568.0 0.152 217568.0 ; CAL CAJ
4 5 1 0.141 267776.0 0.141 267776.0 ; OAI CAK
5 6 1 0.109 284512.0 0.109 284512.0 ; CAK HAB
5 7 1 0.109 284512.0 0.109 284512.0 ; CAK HAG
5 8 1 0.151 234304.0 0.151 234304.0 ; CAK CAM
8 9 1 0.108 284512.0 0.108 284512.0 ; CAM HAF
8 10 1 0.108 284512.0 0.108 284512.0 ; CAM HAH
8 11 1 0.150 217568.0 0.150 217568.0 ; CAM CAJ
11 12 1 0.108 284512.0 0.108 284512.0 ; CAJ HAC
11 13 1 0.108 284512.0 0.108 284512.0 ; CAJ HAA
[ pairs ]
; ai aj fu c0, c1, ...
1 5 1 ; HAD CAK
1 8 1 ; HAD CAM
1 12 1 ; HAD HAC
1 13 1 ; HAD HAA
2 6 1 ; CAL HAB
2 7 1 ; CAL HAG
2 9 1 ; CAL HAF
2 10 1 ; CAL HAH
3 5 1 ; HAE CAK
3 8 1 ; HAE CAM
3 12 1 ; HAE HAC
3 13 1 ; HAE HAA
4 9 1 ; OAI HAF
4 10 1 ; OAI HAH
4 12 1 ; OAI HAC
4 13 1 ; OAI HAA
5 12 1 ; CAK HAC
5 13 1 ; CAK HAA
6 9 1 ; HAB HAF
6 10 1 ; HAB HAH
6 9 1 ; HAB HAF
6 10 1 ; HAB HAH
6 11 1 ; HAB CAJ
7 9 1 ; HAG HAF
7 10 1 ; HAG HAH
7 11 1 ; HAG CAJ
9 12 1 ; HAF HAC
9 13 1 ; HAF HAA
10 12 1 ; HAH HAC
10 13 1 ; HAH HAA
[ angles ]
; ai aj ak fu c0, c1, ...
1 2 3 1 107.8 276.1 107.8 276.1 ; HAD CAL
HAE
1 2 4 1 109.5 292.8 109.5 292.8 ; HAD CAL
OAI
Hello;
the bond angles seem to be respondsible. You use function type 1. That
means you just have a harmonic potential. To this end gromacs wants an
equilibrium angle and a "spring constant". You provide 4 numbers. I
dont the funtions in mind. However for function 1, it shoudl probably
look like :
1 2 11 1 110.7 313.8 ; HAD CAL
However I do not which kind of function you want to chose. All this
information is given in Chapter 5 Topologies. Together with the
information about the calculation of bonded and nondbonded energy terms
you can set up the itp file correctly without any trouble.
Best Regards,
Flo
CAJ
3 2 4 1 109.5 292.8 109.5 292.8 ; HAE CAL
OAI
3 2 11 1 110.7 313.8 110.7 313.8 ; HAE CAL
CAJ
4 2 11 1 109.5 292.8 109.5 292.8 ; OAI CAL
CAJ
2 4 5 1 109.5 502.0 109.5 502.0 ; CAL OAI
CAK
4 5 6 1 109.5 292.8 109.5 292.8 ; OAI CAK
HAB
4 5 7 1 109.5 292.8 109.5 292.8 ; OAI CAK
HAG
4 5 8 1 109.5 292.8 109.5 292.8 ; OAI CAK
CAM
6 5 7 1 107.8 276.1 107.8 276.1 ; HAB CAK
HAG
6 5 8 1 110.7 313.8 110.7 313.8 ; HAB CAK
CAM
7 5 8 1 110.7 313.8 110.7 313.8 ; HAG CAK
CAM
5 8 9 1 114.3 292.8 114.3 292.8 ; CAK CAM
HAF
5 8 10 1 114.3 292.8 114.3 292.8 ; CAK CAM
HAH
5 8 11 1 117.2 313.8 117.2 313.8 ; CAK CAM
CAJ
9 8 10 1 114.3 292.8 114.3 292.8 ; HAF CAM
HAH
9 8 11 1 117.2 313.8 117.2 313.8 ; HAF CAM
CAJ
10 8 11 1 117.2 313.8 117.2 313.8 ; HAH CAM
CAJ
2 11 8 1 117.2 313.8 117.2 313.8 ; CAL CAJ
CAM
2 11 12 1 114.3 292.8 114.3 292.8 ; CAL CAJ
HAC
2 11 13 1 114.3 292.8 114.3 292.8 ; CAL CAJ
HAA
8 11 12 1 117.2 313.8 117.2 313.8 ; CAM CAJ
HAC
8 11 13 1 117.2 313.8 117.2 313.8 ; CAM CAJ
HAA
12 11 13 1 114.3 292.8 114.3 292.8 ; HAC CAJ
HAA
[ dihedrals ]
; ai aj ak al fu c0, c1, m, ...
2 1 3 4 3 1.58 4.769 1.58 4.769 ; imp CAL HAD
HAE OAI
5 4 6 7 3 1.58 4.769 1.58 4.769 ; imp CAK OAI
HAB HAG
8 5 10 9 3 0.62 1.882 0.62 1.882 ; imp CAM CAK
HAH HAF
11 2 12 8 3 0.62 1.882 0.62 1.882 ; imp CAJ CAL
HAC CAM
1 2 4 5 3 1.5 4.7 3 1.5 4.7 3 ; dih HAD CAL
OAI CAK
13 11 2 1 3 1.5 4.7 3 1.5 4.7 3 ; dih HAA CAJ
CAL HAD
2 4 5 8 3 1.5 4.7 3 1.5 4.7 3 ; dih CAL OAI
CAK CAM
11 8 5 4 3 1.5 4.7 3 1.5 4.7 3 ; dih CAJ CAM
CAK OAI
13 11 8 5 3 0.6 1.8 3 0.6 1.8 3 ; dih HAA CAJ
CAM CAK
and I really could not find which parameter should I included.
Thanks
yours,
Morteza
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========================================
Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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--
Florian Dommert
Dipl.-Phys.
Computational and Theoretical Softmatter & Biophysics group
Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University
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