[gmx-users] Re: gmx-users Digest, Vol 81, Issue 126

parthiban at ncbs.res.in parthiban at ncbs.res.in
Thu Jan 20 10:20:22 CET 2011

> Message: 5
> Date: Wed, 19 Jan 2011 08:37:20 -0500
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4D36E910.6030106 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> parthiban at ncbs.res.in wrote:
>> Hi
>> I am using a dimer for my simulation system which is connected by 2
>> disulfide bonds.
>> After energy minimization for even few cycles, the disulfide bond breaks
>> which is not expected.
> Bonds do not break in classical molecular mechanics.  One of two things is
> happening:
> 1. There was never a bond to begin with (check your topology)
There do a bond exists.
> 2. The bond is highly strained, in which case something is wrong with your
> structure.
>> i have applied amber99 force field and prepared the system. while i
>> tried
>> with another force field in Gromacs which did not worked at all.
> What does that mean?  What failed?
As said previously the bond is strained only after pdb2gmx itself. is
there any other way to fix it.

but in gendral the molecule is free from strains.
>> also i have tried by editing specbond.dat as well but of no use.
> In what way?  Have you seen the information at:
> http://www.gromacs.org/Documentation/File_Formats/specbond.dat

i tried to alter the distance of cys bond length by +/-.

> -Justin
>> can any one share/discuss some ideas how to fix this.
>> reg's,
>> Parthiban.

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