[gmx-users] : Incorrect number of parameters - found 4, expected 6 or 12.
Florian Dommert
dommert at fias.uni-frankfurt.de
Wed Sep 10 12:17:06 CEST 2008
* Justin A. Lemkul <jalemkul at vt.edu> [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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Phone: +49(0)69 / 798 - 47522
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