What kind of parameters are you using? Gromacs? Amber? I was told you can check for previous calculations done for S-S bonds in published papers, find its constants, bond length, and all and add them to the bonds' parameter file. Then generate a .gro and a .top. It could work. Just make sure you convert to the appropiate units.
Good luck. ==============Original message text=============== On Tue, 25 Jul 2006 13:59:14 EDT "Cesar Araujo" wrote: Hi, Can anybody tell me how can I generate arbitrary S-S bonds with gromacs? The problem is that I have a protein and I want to specify some S-S bond between two cysteine residues but they are not an options given by pdb2gmx -ss. Should I touch topology file by hand? Why pdb2gmx do not recognizes automatically SSBOND records in pdb files? Regards, César.-===========End of original message text=========== _______________________________________________ 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
