From: Axel Kohlmeyer (
Date: Tue Jul 15 2008 - 13:39:06 CDT

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

MEF> Hi John,
MEF> Thank you for your reply. Perhaps I wasn't clear enough. I'm loading
MEF> my trajectories along with the PSF file. I also tried to create a
MEF> matching psf for the protein and I always get the same result. What
MEF> puzzles me is that I can correctly visualize the original trajectory
MEF> (psf + dcd files).

yes. but how do you "generate" the subset .psf file?
you have to save it from the exact same selection
than what you use for the .dcd file so that the ordering
of atoms does not get messed up.

i usually do

$sel writepsf subset.psf
animate write dcd subset.dcd sel $sel waitfor all

this has always worked for me (and it should).


MEF> Cheers,
MEF> Michel
MEF> On Tue, Jul 15, 2008 at 8:04 PM, John Stone <> wrote:
MEF> >
MEF> > Hi,
MEF> > Rather than loading your processed trajectories with a PDB (which doesn't
MEF> > specify connectivity explicitly) you'd be better off emitting both a
MEF> > processed trajectory as well as a PSF file that contains the explicit
MEF> > connectivity information. The "distorted" residues you were seeing may
MEF> > simply be the result of distance-based bond heuristic doing a bad job
MEF> > with unusual geometry when some of the structure has been removed.
MEF> > Try generating a matching PSF and see if you still have the same problem.
MEF> > If you do, please send me a copy of the original, and modified structure
MEF> > files so I can load them and compare them myself.
MEF> >
MEF> > Cheers,
MEF> > John Stone
MEF> >
MEF> >
MEF> > On Tue, Jul 15, 2008 at 07:50:58PM +0200, L. Michel Espinoza-Fonseca wrote:
MEF> >> Hi all,
MEF> >>
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.
MEF> >>
MEF> >> All comments will be appreciated.
MEF> >>
MEF> >> Cheers,
MEF> >> Michel
MEF> >
MEF> > --
MEF> > NIH Resource for Macromolecular Modeling and Bioinformatics
MEF> > Beckman Institute for Advanced Science and Technology
MEF> > University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
MEF> > Email: Phone: 217-244-3349
MEF> > WWW: Fax: 217-244-6078
MEF> >

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.