VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Oct 27 2009 - 12:37:28 CDT

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