VMD-L Mailing List

From: Krishnan, Marimuthu (krishnanm_at_ornl.gov)
Date: Thu Apr 23 2009 - 10:15:44 CDT

Dear friends,

I would like to calculate the local packing density around a methyl group (or a side chain) of a protein.
The MD trajectory, which was generated using NAMD, of this protein is available. I would appreciate if
someone could direct me to some existing codes/scripts that can do this task.

I would be happy to write a simple code to do this job but I need some clarifications on this topic.
To compute local packing density, I need to know the vdW radii of the chemical group and its neighbors.
I am wondering about contributions from bonded atoms (There is no van der Waals interactions between
atoms involved in a covalent bond, angle and dihedral). The questions are:
(1) How do I get vdW radii of the chemical group( or atoms) and its neighbors?
(2) How do I take care of bonded pair of atoms in the computation of local packing density?

I would appreciate your help and suggestions.

Thanks,
Krishnan

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Dr. Marimuthu Krishnan
Postdoctoral Research Scholar,
Center for Molecular Biophysics,
Oak Ridge National Laboratory,
Building 6011,
PO Box 2008 MS6309,
Oak Ridge, TN 37831-6309,
Tel : 001-865-574-6123
Fax : 001-865-576-7651
E-mail : krishnanm_at_ornl.gov
For more details : http://cmb.ornl.gov/group/kgh
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