VMD-L Mailing List

From: Bob Johnson (bobjohnson1981_at_gmail.com)
Date: Tue Oct 27 2009 - 12:42:06 CDT

Well...the trajectory is from a replica exchange simulation. Thus, there are
discontinuities in the trajectory where the protein coordinates change
rapidly. I have all the coordinates aligned the best I can (i.e. the center
of each protein configuration is situated close to the origin), but the
rapid jumps are still going to be there.

I'm not sure what you mean by "large magnitude atom coordinates".
Thanks,
Bob

On Tue, Oct 27, 2009 at 1:37 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Bob,
> More likely than not, STRIDE is failing due to overruns on one or more
> of the PDB per-atom data fields, e.g. due to large magnitude atom
> coordinates
> which can often occur within long trajectories. Does the problem go away
> if
> you align your trajectory frames to a reference where the reference frame
> is situated around the origin?
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Oct 27, 2009 at 01:22:03PM -0400, Bob Johnson wrote:
> > Hello everyone,
> > I'm performing some analysis on peptide conformations over the course
> > of a trajectory. I use "mol ssrecalc 0" on each frame and write the
> > secondary structure information to a file with "$sel get structure".
> > This seems to work fine...except that for many frames I obtain the
> > following error messages:
> > ERROR) Unable to find Stride output file: /usr/tmp/fileukCAna
> > ERROR) Stride::read_stride_record: unable to read output file from Stride
> > ERROR) Call to Stride program failed
> >
> > This doesn't happen for every frame, but it happens often enough that
> > I'm wondering what's going on. VMD can read my PDB input file fine -
> > the structure doesn't have any connectivity defects. What is causing
> > the error messages?
> > Thanks,
> > Bob
> >
> > --
> > Bob Johnson, PhD
> > Institute for Computational Molecular Science
> > Temple University
> > 1900 North 12th Street
> > Philadelphia, PA 19122
> > http://www.sas.upenn.edu/~robertjo>
>
> --
> 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/ <http://www.ks.uiuc.edu/%7Ejohns/>
> Fax: 217-244-6078
> 

-- 
Bob Johnson, PhD
Institute for Computational Molecular Science
Temple University
1900 North 12th Street
Philadelphia, PA 19122
http://www.sas.upenn.edu/~robertjo