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

Roland Schulz roland at utk.edu
Wed Aug 25 19:05:27 CEST 2010


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


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.
> Thanks
> Rabab--
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