[gmx-users] Re: Problem in Disulfide Bond

[Mark Abraham]

On 01/20/11, parthiban at ncbs.res.in wrote:
> > 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.
> 

So you can see in your [bonds] section an entry for the two atom numbers?


> 
> > 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.
> 

Previously you said the bond was strained after EM. pdb2gmx is not capable of straining a bond.

Be sure you are not looking at "bonds" generated via heuristics in some visualization program. If pdb2gmx is generating a disulfide bond, it will say so in the standard output, and you will be able to find it in the [bonds] section. Otherwise, there is no bond.

Mark


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