Hi, VMD was built to work with NAMD, so the atom names and topologies will not work with GROMACS. I guess you better go to Peter Tieleman site ( http://moose.bio.ucalgary.ca/) and rad there how to do things.
Cheers, Itamar On Tue, Nov 10, 2009 at 8:05 AM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > parthi...@ncbs.res.in wrote: > >> Hi >> >> I have constructed the bilayer with protein molecule in VMD. >> >> Can any one tell how to start MD from here. >> > > Follow the methods of whichever tutorial you learned from :-) > > > the initial step - pdb2gmx is not working for this complex(pdb+membrane) >> > > We're not omniscient... tell us what you did, what you expected, what you > saw and why you think it was not working :-) > > Mark > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
