VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jul 15 2008 - 12:50:58 CDT

Hi all,

In the past few days I've been analyzing MD trajectories generated by
NAMD. I've been able to load the trajectories and visualize the
systems without any problem. However, when I write out a DCD-formatted
trajectory of the protein only and visualize it with the latest
version of VMD, *all* the N-epsilon-protonated histidines look
completely distorted. First I thought it could be a problem related to
my original psf files, but I was able to write out pdb-formatted
trajectories of the protein alone. Even if I want to write out a dcd
file from the pdb-formatted trajectory, the problem appears again.
Thus, I suspect that the problem might be related directed to the
engine that allows VMD to write dcd files. It is also important to
mention that I've been testing VMD on different platforms (Linux,
windows and mac), and I always got the same result.

All comments will be appreciated.

Cheers,
Michel