questions about set cellBasisVector and a ligand ...

From: Xiaobing Tian (
Date: Thu Apr 29 2004 - 10:06:53 CDT

Dear everyone,

I started to do MD using namd. But there are several questions I am not
1. How do I set cellBasisVector1,2 and 3 for a specific protein?
There are not instructions about this in both namd manual and tutorial.
2. My system is a protein/drug. I only have x-plor topology and
parameter files for the ligand. Could I use CHARMM topology and
parameter files for my protein and X-PLOR files for my ligand ? If I
have to use X-PLOR files, where can I download them ?
3. After generate my ligand psf and pdb files using psfgen, how can I
combine the ligand psf file with the protein psf file?

Thank you very much for your time.

Xiaobing Tian, Ph.D.
Department of Biochemistry & Molecular Pharmacology
Thomas Jefferson University
233 South 10th Street, Suite 219
Philadelphia PA19107
voice: 215-955-1364   fax: 215-955-4580, 215-923-9214

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