From: Axel Kohlmeyer (
Date: Tue Jul 15 2008 - 13:21:57 CDT

On Tue, 15 Jul 2008, L. Michel Espinoza-Fonseca wrote:

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


where do you get the bonding information for the reduced
.dcd file from? did you write out a matching .psf file?

i have not seen anything like it and i don't see
a reason why it should happen only to one specific
residue type.


MEF> All comments will be appreciated.
MEF> Cheers,
MEF> Michel

Axel Kohlmeyer
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
If you make something idiot-proof, the universe creates a better idiot.