Hi Ram, Check the option -merge of pdb2gmx.
Cheers, Tsjerk On Thu, Jun 26, 2008 at 6:11 AM, rams rams <[EMAIL PROTECTED]> wrote: > Dear Gromacs users, > > Is there any way to handle the disulphide bond formed between two > independent fragments of a protein ? Precisely it is an inter disulphide > bond between two fragments. If I keep the two fragments as separate objects > while preparing the pdb file (using TER between the two fragments), gromacs > is not asking for the formation of a disulphide bond. If I keep them as a > single object while preparing the input pdb, gromacs could recognize the > disulphide bond but while running the energy minimization its complaining > that the distances are too close. > > Is there any way to handle these ? I am also thinking like keep them as > separate objects and imposing positional restraints on both the sulphur > atoms. Is it all right to do that way ? > > Please suggest me some thing how to handle these ? > > Ram. > > _______________________________________________ > gmx-users mailing list [email protected] > 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 > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 _______________________________________________ gmx-users mailing list [email protected] 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
