Hello,<br><br>I just changed the disulfide max bond length in the specbond.dat file to various numbers (0.4, 0.5, 1.2, 8.0, ...) and pdb2gmx only assigns some of the disulfides in my protein but not all. If I use 0.4, it finds 22 of the 52 CYS residues to be in disulfide bonds when all 52 should be in disulfide bonds. And, if I use higher bond lengths the number of disulfide CYS found decreases. Where should I look next to sort out this problem?
<br><br>Thanks,<br>Russell Green<br><br><div><span class="gmail_quote">On 7/1/07, <b class="gmail_sendername">Mark Abraham</b> <<a href="mailto:mark.abraham@anu.edu.au">mark.abraham@anu.edu.au</a>> wrote:</span><br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><br>Did you use specbond.dat correctly?<br><a href="http://wiki.gromacs.org/index.php/specbond.dat">
http://wiki.gromacs.org/index.php/specbond.dat</a><br><br>Mark<br><br>_______________________________________________<br>gmx-users mailing list <a href="mailto:gmx-users@gromacs.org">gmx-users@gromacs.org</a><br><a href="http://www.gromacs.org/mailman/listinfo/gmx-users">
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