From: Jacopo Sgrignani (
Date: Thu Jul 14 2011 - 11:05:37 CDT

VMD users I would like to use the Implicit Ligand Sampling plugin but I'm
new to this an I have some questions.
I've already run an MD simulation using NAMD and an amber prmtop file, how
can I run the implicit ligand calculation?
Do I need to setup charmm parameters?
Do I have to remove the explicit waters?

I found some papers where they have used MD trajectories, generated using
Amber parameters to do this calculation for HEME proteins, but i can not
understand how they have used the force field parameters with the VMD
ILS plugin.

Can somebody give me some advices?