VMD-L Mailing List

From: Robert Kretschmer (robert.kretschmer_at_freenet.de)
Date: Mon Dec 18 2006 - 12:55:20 CST

Dear all,

I'd like to do a molecular dynamics simulation of a complex of ligand and protein. I could not find a tutorial about it.
But let me explain what i want do to:
I have two crystalstructures of an enzyme - one without a ligand and one with a ligand. In the second one you can see very good the "induced fit" of some PHE-residues.
I want to model the occurence of closing the binding site. It is possible to do this with namd? Exist a tutorial about this type of MD-Simulation?

Thank you very much, kind regards and happy holiday (a friend told me "Don't say merry christmas - many lawers wait for this "discrimination against X-mas free cultures"")

robert