<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font face="Lucida Grande" size="3" style="font: 11.0px Lucida Grande">Dear GROMACS Users,</font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;">I want to do MD of insulin monomer (first two chain of 4ins.pdb). When I convert with pdb2gmx, the software find only one ss bond (the only inside the same chain). I have resolved this problem doing a first conversion pdb->gro, then gro->pdb end in the final conversion pdb->gro the software find the all three ss bond, and number the residues of the two chain like one.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br class="webkit-block-placeholder"></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;">But now there is the big problem, when I do a two step minimization (for bad contacts) the two chain go away, like no ss bonds exist.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;">Whit VMD I can see that all the S atoms is on one chain (the first, whit have the internal SS bond). Then there are two CYS with two S atoms and two (on the other chain) with no S atom.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;">I have cecked the topology file, and the bond between CB and S, and S-S are all correct.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br class="webkit-block-placeholder"></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;">I think that the problem is inside the two chain configuration, but I haven't explanation for the CYS without S.</span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;"><br class="webkit-block-placeholder"></span></font></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><font class="Apple-style-span" face="'Lucida Grande'" size="3"><span class="Apple-style-span" style="font-size: 11px;">Thanks</span></font></div>
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