From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 27 2009 - 12:45:16 CDT

Bob,
  What I mean by "large magnitude coordinates" are coordinates whose
absolute value is large enough that printing it as a text field within
a PDB exceeds the number of characters allotted for the coordinate fields.
For example 1234567890123456789.0 or -1234567890123456789.0 :-)

Cheers,
  John

On Tue, Oct 27, 2009 at 01:42:06PM -0400, Bob Johnson wrote:
> 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/ 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

-- 
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