VMD-L Mailing List

From: Falgun Shah (fhshah_at_olemiss.edu)
Date: Sun Mar 01 2009 - 15:23:12 CST

Dear Vmd users

I am doing constant velocity smd simulation of the protein of my interest. I
want to generate final image of the protein in surface representation along
with virtual spring showing 3 direction of egress for my ligand. Please let
me know the best way to generate molecular surface of protein binding site
and how to insert spring between COM of the smd atoms and the calculated
direction. Your recommendations are most welcome. Thanks in advance. 

-- 
Falgun H shah
PhD candidate (3rd year)
Department of Medicinal Chemistry
2028, Natural Product Center
University of Mississippi
Ph No: 6629151286(O)
          662 801 5667(M)
email: fhshah_at_olemiss.edu