[gmx-users] How to tell if the molecule is correctly reduced?

Justin A. Lemkul jalemkul at vt.edu
Thu Aug 26 22:37:53 CEST 2010

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:



> Rabab Toubar
> --- On *Wed, 8/25/10, Mark Abraham /<mark.abraham at anu.edu.au>/* wrote:
>     From: Mark Abraham <mark.abraham at anu.edu.au>
>     Subject: Re: [gmx-users] How to tell if the molecule is correctly
>     reduced?
>     To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
>     Date: Wednesday, August 25, 2010, 8:57 PM
>     ----- Original Message -----
>     From: Roland Schulz <roland at 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 at 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
>     <rtoubar at 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
>     -----Inline Attachment Follows-----
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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