[gmx-users] Re: Problem in Disulfide Bond

[Oliver Grant]

Show us that part of your topology. When you used ffamberports have you
renamed the CYS to CYS2?

Oliver

On 20 January 2011 09:23, <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.
> > 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 +/-.
>  reg,
> Parthi.
>
> > -Justin
> >
> >> can any one share/discuss some ideas how to fix this.
> >>
> >> reg's,
> >> Parthiban.
> >>
>
>
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