VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jul 15 2008 - 13:44:13 CDT

Hi Axel,

Thank you for the suggestion. I'll give it a try and will let you know
if I the problem still appears.

Cheers,
Michel

On Tue, Jul 15, 2008 at 8:39 PM, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> On Tue, 15 Jul 2008, L. Michel Espinoza-Fonseca wrote:
>
> MEF> Hi John,
> MEF>
> 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).
>
> cheers,
> axel.
>
> MEF>
> MEF> Cheers,
> MEF> Michel
> MEF>
> MEF> On Tue, Jul 15, 2008 at 8:04 PM, John Stone <johns_at_ks.uiuc.edu> 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> > vmd_at_ks.uiuc.edu
> 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: johns_at_ks.uiuc.edu Phone: 217-244-3349
> MEF> > WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
> MEF> >
> MEF>
>
> --
> =======================================================================
> Axel Kohlmeyer akohlmey_at_cmm.chem.upenn.edu http://www.cmm.upenn.edu
> 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.
>