I use the option -merge with my SS-linked peptides, and pdb2gmx always asks me if I want to join my cysteines with a bond. If they're internal to the protein, perhaps it's either that they're too far apart, or you need -ignh as otherwise they've got hydrogens on and potentially can't bond.
--- Cesar Araujo <[EMAIL PROTECTED]> wrote: > Hi, > > Anybody knows if there is some way to tell pdb2gmx > to recognize automatically S-S bonds and not through > the modification of specbond.dat file and -ss > option??? > > Regards, > César.- > > ----------------------------------------------------------- > Cesar Araujo, Lic. of Chemistry > Department of Molecular Endocrynology > Oulu University Hospital > FIN-90029 OYS, FINLAND > > phone: +358 8 3155632 > e-mail: [EMAIL PROTECTED] > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > 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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
