From: Shulin Zhuang (shulin.zhuang_at_gmail.com)
Date: Fri Aug 03 2007 - 02:31:22 CDT
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.
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!
-- Shulin Zhuang, Ph.D. Dr. Hongbin Li's group Department of Chemistry University of British Columbia 2036 Main Mall Vancouver, BC, Canada V6T 1Z1 Email:shulin.zhuang_at_gmail.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:02 CST