Hi Sridhar, pdb2gmx adds all hydrogens _according to the force field definition_ (and a database file describing how to add which hydrogen where). If you want to have all hydrogens "satisfying the valencies", you need to choose a force field that includes them, i.e. an all-atom force field. Maybe it would be good to read a bit more about united atom / all atom force fields and such.
Cheers, Tsjerk On Thu, Aug 14, 2008 at 5:56 PM, sridhar acharya <[EMAIL PROTECTED]> wrote: > Hi, > > The manual says, pdb2gmx adds all hydrogens, including those for carbons. > But I could not find the output gro file to contain all the hydrogens > (especially for carbons) satisfying all the valencies. Is there any option > that I may be missing? > > thanks, > > _______________________________________________ > 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
