Hi Amit, You don't need to convert the .pdb file. Gromacs can handle several file formats, including .pdb. If you have a topology that matches the .pdb in terms of atoms, then you can simply proceed with the subsequent steps. pdb2gmx is not exactly meant to convert the structure file to another file format, but to generate a topology for a system built up of well defined blocks and, if necessary, edit the structure to match the force field.
Cheers, Tsjerk On Thu, Sep 10, 2009 at 2:29 AM, Amit Choubey <kgp.a...@gmail.com> wrote: > hi everyone, > I have a pdb file of my system and i want it to be fed into the GROMACS > software. I have a new force field for the simulation and i have made the > .top file manually which includes the new library FF files. I need to get a > .gro file from the .pdb file that i have. So, is there a way out to do this > without incorporating pdb2gmx because i dont use the standard FF and i dont > really have all the other datafiles for the new FF except for necessary bond > and nonbonded infos. > Amit > _______________________________________________ > gmx-users mailing list gmx-us...@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 > -- 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 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
