VMD-L Mailing List

From: Bob Johnson (bobjohnson1981_at_gmail.com)
Date: Tue Oct 27 2009 - 12:47:55 CDT

I see...yes I don't think that is the problem. The center of the protein is
close to the origin and doesn't extend beyond 30 angstroms in any direction.
Bob

On Tue, Oct 27, 2009 at 1:45 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

> 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/ <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