VMD-L Mailing List

From: pkmukher (pkmukher_at_olemiss.edu)
Date: Thu Mar 08 2007 - 21:36:49 CST

Hello VMD users

I am a new user of VMD. I want to carry out a particular
orientation operation on my molecule(protein-ligand complex)
 In my case the ligand is situated in a cavity on the
surface of the protein. I intend to carry out a steered
molecular dynamics study. For this i require the
protein-ligand complex to be oriented such that the force
vector from the protein atom to the ligand atom be parallel
to two of the axis. That way when i construct the solvent
box i can keep it more elongated on the third axis to
accomodate for the ligand movement once it comes out of the
binding site.
As an alternative I tried to use the orient script which
orients on the basis of principle moments but i was not
successful. Is there a way to define the principle moments
on the basis of the ligand but carry out the reorientation
for the whole complex. Currently when i defined the
principle axis on the basis of the ligand it reoriented only
the ligand.

Thanks so much

Prasenjit Kumar Mukherjee
Graduate Student
Department of Medicinal Chemistry
School of Pharmacy
University of Mississippi
USA

Cell - 662 380 0146
Office - 662 915 1286