Assign the ligand force field parameters

From: Grace Shen (Lingling.Shen_at_bnpi.com)
Date: Mon Oct 24 2005 - 16:32:13 CDT

Dear All:

Does anyone happen to know if there is a way for me to assign my ligand
(which is not in charmm parameter file) force field parameters automatically
(not manually)?

-----Original Message-----
From: Raul Araya Secchi [mailto:arayasecchi_at_hotmail.com]
Sent: Monday, October 24, 2005 3:21 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: Water Sphere

Dear NAMD Users:

Im triying to perform an alchemical FEP calculation to asses the effect of a
mutation in the binding free energy of a protein-protein complex but I dont
want to put the whole complex into a water box and use Periodic Boundary
Conditions, because it will make my calculations to slow. So I was wanderin
how can I put a sphere of water arround the interaction interface and keep
the rest of the protein with harmonic constrains and a dielectric constant
to replace the slovent.

Thanks

Raul Araya
Center for Genomics and Bioinformatics
Catholic University of Chile
Santiago
Chile

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