Rabab Toubar wrote:
Thanks Roland and Mark for your input.
I did pdb2gmx -ss and checked the top file where the Cys are represented
as CYSH, but when I loaded the generated pdb file in vmd, I can still
see the original dsulfides bond, and each sulfur is protonated. Is this
an artifact? Is there another way to confirm that the molecule is
properly reduced
Whatever is in the topology is what is actually used for the simulation. As for
VMD trying guess bonds, please see FAQ #9:
http://www.gromacs.org/Documentation/FAQs
-Justin
Rabab Toubar
--- On *Wed, 8/25/10, Mark Abraham /<mark.abra...@anu.edu.au>/* wrote:
From: Mark Abraham <mark.abra...@anu.edu.au>
Subject: Re: [gmx-users] How to tell if the molecule is correctly
reduced?
To: "Discussion list for GROMACS users" <gmx-users@gromacs.org>
Date: Wednesday, August 25, 2010, 8:57 PM
----- Original Message -----
From: Roland Schulz <rol...@utk.edu>
Date: Thursday, August 26, 2010 3:06
Subject: Re: [gmx-users] How to tell if the molecule is correctly
reduced?
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
> Hi,
> if the gro file written by pdb2gmx contains the same number of
hydrogens then before, than you disulfide bonds haven't changed.
pdb2gmx automatically forms disulfide bridges if the atoms are
within some distance (see specbond). Look at the output of pdb2gmx
and make sure it is doing what you expect/want.
>
> Roland
>
> On Wed, Aug 25, 2010 at 12:44 PM, Rabab Toubar
<rtou...@yahoo.com> wrote:
> Hi
>
> I did simulations for a protein with disulfide bonds using
opls. Then I reduced the ssbonds in vmd and did simulations for
the reduced. When loading gro(or pdb) and trr files on vmd I do
not see reduced bonds. I also compared the two pdb files and
they looked the same in terms of number of hydrogens in
cysteines. So how can I tell if the molecule is properly reduced
before going further.
It can't be "properly reduced" by VMD. The coordinates and the
topology both have to change, and VMD neither reads or writes .tpr
and .top.
Instead, use pdb2gmx -ss to allow you to choose which disulfides are
made in the first place.
Mark
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--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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