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

Mark Abraham mark.abraham at anu.edu.au
Thu Aug 26 02:57:48 CEST 2010

----- 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.


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