[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 10 11:46:07 CEST 2008
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
> 1 2 11 1 110.7 313.8 109.5 397.5 ; HAD CAL 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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