[gmx-users] postdocking MD?

[Peter C. Lai]

Sorry for being a newbie, but I am trying to use gromacs
to look at ligand-receptor interaction. I generated
coordinates for the ligand via a docking program and I merged
them with the receptor pdb. The ligand is listed as UNK in the pdb,
and pdb2gmx doesn't like it (unknown residue UNK).
Should I alter to pdb to list the ligand as a heteroatom record? 
What is the best way to go about this? The documentation covers
MD of a single protein in a solvent; I'm trying to get a trajectory
of a ligand in its binding pocket...

thanks,
pete

-- 
Peter C. Lai
University of Connecticut
Dept. of Molecular and Cell Biology | Undergraduate Research Assistant
Yale University School of Medicine
Center for Medical Informatics | Research Assistant
http://cowbert.2y.net/