How to calculate the C alpha RMSD from NAMD trajectory

From: Shulin Zhuang (
Date: Fri Aug 03 2007 - 02:31:22 CDT

Dear All,

I just do a MD simulations of a small protein using NAMD soft, now, I want
to calculate the C alpha RMSD of the protein from the trajectory. Using VMD,
only the backbone RMSD can be calculated.

Another question:
For hydrogen analysis, how to calculate the hydrogen bond like soft PTRAJ.
PTRAJ can easily calculate many kind of RMSD from Amber or charmm
trajectory. How can we use ptraj to analyze trajectory produced by NAMD.

Wish you will give me any help!
Best regards

Shulin Zhuang, Ph.D.
Dr. Hongbin Li's group
Department of Chemistry
University of British Columbia
2036 Main Mall
Vancouver, BC, Canada  V6T 1Z1

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:02 CST