VMD-L Mailing List

From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Tue Jul 15 2008 - 13:08:55 CDT

Hi John,

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

Cheers,
Michel

On Tue, Jul 15, 2008 at 8:04 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> 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.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>