[gmx-users] Missing VdW Parameters

[darrellk at ece.ubc.ca]

Hi All,
I did not receive a response yet for my question below, so I am
submitting it once again.

Thanks again in advance for your help.

Darrell

On 4/12/2009, "<darrellk at localhost>" <> wrote:

>Hi All,
>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 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
>>
>>
>>------------------------------