[gmx-users] OPLS force field does not recognize Atom type
Florian Dommert
dommert at fias.uni-frankfurt.de
Tue Sep 9 22:49:38 CEST 2008
* Morteza Khabiri <khabiri at greentech.cz> [2008-09-09 22:03:36 +0200]:
>Dear
>I want to make the solution which is not working with unified atom force
>fields. Then I decided to make the itp file by my own.
>I made the all atom type ....itp file for opls AA. I found all of the opls
>feature in gromacs top directory and according to the top directory files
>I made the new itp file. Unfortunately, after running the grompp i faced
>with the following error:
> Fatal error:
> Atomtype 'HC' not found!
>but it is defined in the opls.
>
>My itp file structure is like follow:
>;
>[ moleculetype ]
>; Name nrexcl
>DRG 3
>
>[ atoms ]
>; nr type resnr resid atom cgnr charge mass
> 1 HC 1 DRG HAD 1 0.02734 1.0080
> 2 CT 1 DRG CAL 1 0.10638 12.0110
Hello,
your faulty itp file results from the string in the second column. It
should correspond to the OPLS atom nr, like opls_032.
Best Regards,
Flo
> 3 HC 1 DRG HAE 1 0.02734 1.0080
> 4 OS 1 DRG OAI 1 -0.36111 15.9994
> 5 CT 1 DRG CAK 1 0.10638 12.0110
> 6 HC 1 DRG HAB 2 0.02734 1.0080
> 7 HC 1 DRG HAG 2 0.02734 1.0080
> 8 CY 1 DRG CAM 2 0.00235 12.0110
> 9 HC 1 DRG HAF 3 0.00857 1.0080
> 10 HC 1 DRG HAH 3 0.00857 1.0080
> 11 CY 1 DRG CAJ 3 0.00235 12.0110
> 12 HC 1 DRG HAC 3 0.00857 1.0080
> 13 HC 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
> 6 9 1 ; HAB HAF
> 8 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
>
>
>The top file is also set to OPLS forcefield.
>
>I don't know what is wrong exactly. Thats very nice of you if you could
>help me.
>
>Thank you very much in advance
>
>Morteza
>
>
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--
Florian Dommert
Dipl.-Phys.
Computational and Theoretical Softmatter & Biophysics group
Frankfurt Institute for Advanced Studies
Johann-Wolfgang-Goethe University
Ruth-Moufang-Str. 1
60438 Frankfurt am Main
Phone: +49(0)69 / 798 - 47522
Fax: +49(0)69 / 798 - 47611
EMail: dommert at fias.uni-frankfurt.de
Home: http://fias.uni-frankfurt.de/~simbio/Florian_Dommert
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