[gmx-users] Missing VdW Parameters

[darrellk at ece.ubc.ca]

Hi David,
Yes, indeed, the topology file does have the #include statement. Here is
an extract from the topology file:
***************************************************************************
; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
ICE                 3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass 
typeB    chargeB      massB
     1   opls_145      1   Grph     CA      1          0     12.011   ;
qtot 0
***************************************************************************
Please advise on what may be the problem.

Thanks.

Darrell

>Date: Sun, 12 Apr 2009 07:34:46 +0200
>From: David van der Spoel <spoel at xray.bmc.uu.se>
>Subject: Re: [gmx-users] Missing VdW Parameters
>To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>Message-ID: <49E17D76.6000600 at xray.bmc.uu.se>
>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>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
>
>
>------------------------------