Re: vmd-l: How to calculate the C alpha RMSD from NAMD trajectory

From: John Stone (
Date: Fri Aug 03 2007 - 10:58:13 CDT


On Fri, Aug 03, 2007 at 03:31:22PM +0800, Shulin Zhuang wrote:
> 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.

Please see the VMD tutorials and the User's Guide.
You can make arbitrary atom selections for which 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.

You could use CatDCD or VMD to convert a NAMD DCD trajectory into a format
supported by PTRAJ, that's the best thing that comes to mind. You might check
to see if PTRAJ already supports DCD files, it might do so already.

  John Stone

NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email:                 Phone: 217-244-3349
  WWW:      Fax: 217-244-6078

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