From: John Stone (
Date: Tue Jul 15 2008 - 13:04:18 CDT

  Rather than loading your processed trajectories with a PDB (which doesn't
specify connectivity explicitly) you'd be better off emitting both a
processed trajectory as well as a PSF file that contains the explicit
connectivity information. The "distorted" residues you were seeing may
simply be the result of distance-based bond heuristic doing a bad job
with unusual geometry when some of the structure has been removed.
Try generating a matching PSF and see if you still have the same problem.
If you do, please send me a copy of the original, and modified structure
files so I can load them and compare them myself.

  John Stone

On Tue, Jul 15, 2008 at 07:50:58PM +0200, L. Michel Espinoza-Fonseca wrote:
> 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

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