[gmx-users] OPLS force field does not recognize Atom type
Justin A. Lemkul
jalemkul at vt.edu
Tue Sep 9 22:30:24 CEST 2008
Morteza Khabiri wrote:
> 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.
>
How so? If you look in ffoplsaa.atp, you will note that all atomtypes are
defined as opls_XXX.
-Justin
> 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
> 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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--
========================================
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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