<DIV> </DIV><DIV> </DIV><SPAN>On 16/01/12, pithevenet@free.fr wrote:</SPAN>
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<DIV class="mimepart text plain">Dear all,<br /><br />I'm using the old 3.3.3 version of gromacs and I try to use the -ss option of pdb2gmx to select interactively the ss bridge in my protein.<br /><br />But I don't remark any change between using -ss option and not using it. The -inter option give me some interactive options such as lys or arg but not ss interactive selection.<br /><br />Could you help me?<br /></DIV></BLOCKQUOTE>
<DIV>There are various possible reasons, including that the distance criterion is not met, or that your cysteine residues are in different soon-to-be moleculetypes. Unfortunately you haven't provided enough detailed description of your system or your pdb2gmx command line or its output for anyone to work with.</DIV><DIV> </DIV><DIV>You should be sure to have a compelling scientific reason for wanting to use 3.3.3. Performance and useability are much higher with modern versions. </DIV><DIV> </DIV><DIV>Mark </DIV>