Quoting "P.R.Anand Narayanan" <[email protected]>:
> Dear Gromacs users, > I am planning to bind a ligand to a protein and use gromacs to run the > simulations. But for using the pdb2gmx command, i heard we have to remove all > the ligands and cofactors associated with the protein. While pasting the > necessary parts of the ligand into the gro file, i heard that the bonds would > be broken. Is this true? and if yes are there methods to run the pdb2gmx > command with the ligand. Or the same command without the ligand but not > breaking the bond after pasting it back. > Pls help There is a tutorial on the Gromacs site for protein-ligand simulations. I suggest you look through it. If your ligand is covalently bound, you have an entirely different (and somewhat more difficult) issue. -Justin > > Anand > > > > The INTERNET now has a personality. YOURS! See your Yahoo! Homepage. > http://in.yahoo.com/ ======================================== Justin A. Lemkul Graduate Research Assistant Department of Biochemistry Virginia Tech Blacksburg, VA [email protected] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
