Hi,<div><br></div><div>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.</div>
<div><br></div><div>Roland<br><br><div class="gmail_quote">On Wed, Aug 25, 2010 at 12:44 PM, Rabab Toubar <span dir="ltr"><<a href="mailto:rtoubar@yahoo.com">rtoubar@yahoo.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi<br>
<br>
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.<br>
<br>
Thanks<br>
Rabab--<br>
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