From: Rachel (
Date: Tue Jun 26 2007 - 10:56:34 CDT

Dear all,

I have installed VMD1.8.6, as I read the documents about volmap, it supports
ligand volmap which I am interested in. However, it is not in the volmap

I read the paper by Cohen, J., A. Arkhipov, R. Braun and K. Schulten,
"Imaging the migration pathways of CO, NO, and Xe or O[image: $_2$],inside
myoglobin", Biophysical Journal 91, 1844-1857, 2006. What I want to do is
look at the gas migration pathways inside a different protein which is
similar to that paper. As the author used CHARMM force field in NAMD for the
molecular dynamics, also in the volmap document it says "Before starting the
computation, the atomic radii of each atom should be set to the
corresponding CHARMM Lennard-Jones Rmin/2 parameter (in Angstroms), and the
beta value of each atom should be set to the CHARMM Lennard-Jones epsilon
(energy well depth in kcal/mol) parameter", however, the current package I
am using is AMBER, can I ask is it possible to use the AMBER MD output to
generate such ligand volmap in VMD? will there be any differences? And if
it is compatible with AMBER results, can I ask are there any more detailed
documents about using volmap and making corresponding nice pictures?

Thank you all for any suggestions.