[gmx-users] Re: Problem in Disulfide Bond

[Mark Abraham]

On 01/20/11, parthiban at ncbs.res.in wrote:
> > Message: 3
> > Date: Thu, 20 Jan 2011 09:30:00 +0000
> > From: Oliver Grant <olivercgrant at gmail.com>
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID:
> > 	<AANLkTin5r=+mn5edW=ZqdhRu8fAcoQEdoViXC8X28StC at mail.gmail.com>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> > Show us that part of your topology. When you used ffamberports have you
> > renamed the CYS to CYS2?
> >
> > Oliver
> >
> 
> could you explain this in detail where this change have to done.? i can
> check again.
> 
> > ------------------------------
> >
> > Message: 4
> > Date: Thu, 20 Jan 2011 20:54:39 +1100
> > From: Mark Abraham <mark.abraham at anu.edu.au>
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <7690be842aff.4d38a10f at anu.edu.au>
> > Content-Type: text/plain; charset="iso-8859-1"
> >
> >
> >
> >> > 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?
> 
> I cant see any corresponding entry with res.to CYS residues.
> 

So you didn't make a bond. Anything you saw in pymol or vmd is irrelevant. They didn't read your .top file and that's what counts. You need to call pdb2gmx properly.

Mark

> >
> >
> >>
> >> > 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
> >
> 
> I used pymol and vmd to visualize this
> 
> Thanks
> Parthiban.
> 
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