Hello, 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?
Thanks, Russell Green On 7/1/07, Mark Abraham <[EMAIL PROTECTED]> wrote:
Did you use specbond.dat correctly? http://wiki.gromacs.org/index.php/specbond.dat Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
_______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
