In the pdb, before pdb2gmx, rename the CYS residues involved in the S-S
bonds as CYS2.
If you don't know this then you need to read everything on this page about
using the amberports:
http://ffamber.cnsm.csulb.edu/
As you may have other issues with HIS and LYS residues.
Oliver
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gmx-users mailin
On 01/20/11, parthi...@ncbs.res.in wrote:
> > Message: 3
> > Date: Thu, 20 Jan 2011 09:30:00 +
> > From: Oliver Grant
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users
> > Message-ID:
> >
parthi...@ncbs.res.in wrote:
Message: 3
Date: Thu, 20 Jan 2011 09:30:00 +
From: Oliver Grant
Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
To: Discussion list for GROMACS users
Message-ID:
Content-Type: text/plain; charset="iso-8859-1"
Show us that pa
> Message: 3
> Date: Thu, 20 Jan 2011 09:30:00 +
> From: Oliver Grant
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users
> Message-ID:
>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Show us t
On 01/20/11, parthi...@ncbs.res.in wrote:
> > Message: 5
> > Date: Wed, 19 Jan 2011 08:37:20 -0500
> > From: "Justin A. Lemkul"
> > Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> > To: Discussion list for GROMACS users
> > Message-ID: &l
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, wrote:
> > Message: 5
> > Date: Wed, 19 Jan 2011 08:37:20 -0500
> > From: "Justin A. Lemkul"
> > Subject: Re: [gmx-users] Re
> Message: 5
> Date: Wed, 19 Jan 2011 08:37:20 -0500
> From: "Justin A. Lemkul"
> Subject: Re: [gmx-users] Re: Problem in Disulfide Bond
> To: Discussion list for GROMACS users
> Message-ID: <4d36e910.6030...@vt.edu>
> Content-Type: text/plain; charset=ISO
parthi...@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
hap
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.
i have applied amber99 force field and prepared the system. while i tried
with another force field in Gromacs whic
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