From: Jacopo Sgrignani (sgrigna_at_sissa.it)
Date: Thu Jul 14 2011 - 14:50:21 CDT

Dear
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?

Thanks

Jacopo

----------------------------------------------------------------
   SISSA Webmail https://webmail.sissa.it/
   Powered by Horde http://www.horde.org/