[gmx-users] Missing VdW Parameters

[David van der Spoel]

darrellk at ece.ubc.ca wrote:
> Dear All,
> I successfully ran the x2top command (x2top -ff select -f graphene_nm.gro
> -o graphene_nm.top) and generated a topology using ffoplsaa, but my
> topology is missing VdW parameters, which I thought should be appearing
> in the [ pairs ] section of the topology file. I thought that x2top
> would use the VdW parameters in ffoplsaanb.itp to populate the [ pairs ]
> section of the topology file. But this appears not to be the case.
> Please advise what may be the problem.
> 
> To help diagnose this problem, I am including a portion of the .gro file,
> the relevant section of the .n2t file, and a portion of the [ pairs ]
> section from the generated topology file.

is there a
#include "ffoplsaa.itp"
statement in the top file ?


> 
> selection from .gro file:
>     2Grph C 1 0.000 0.000  0.000 0.0000 0.0000 0.0000
>     2Grph C 2 0.071 -0.123 0.000 0.0000 0.0000 0.0000
>     2Grph C 3 0.071 0.123  0.000 0.0000 0.0000 0.0000
> 
> relevant section of .n2t file:
> C opls_145 0     12.011 3 C 0.140 C 0.140 C 0.140
> C opls_145 -0.06 12.011 3 C 0.140 C 0.140 H 0.108
> C opls_145 -0.12 12.011 3 C 0.140 H 0.108 H 0.108
> H opls_146 0.06   1.008 1 C 0.108
> 
> selection from generated topology file:
> [ pairs ]
> ; ai aj funct c0 c1 c2 c3
>     1 11 1
>     1 12 1
>     1 13 1
>     1 14 1
> 
> Much thanks in advance.
> 
> Darrell
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se