VMD-L Mailing List

From: dimka (newyorkdimka_at_gmail.com)
Date: Fri Nov 18 2005 - 14:50:04 CST

I think it definitely has something to do with the the length of the
trajectory/dcd file size. The trajectory has 500 frames. When I load
all 500 I get the error described. When I load first or last 475
frames everything works fine. But when I load first or last 480
frames that's when the things start to break down and I get the error
again.

If you want I can post the trajectory (711mb) along with the topology
file for your review.

PS. this trajectory was generated using namd with "wrapAll",
"wrapNearest", and "wrapWater" options turned on.

On 11/18/05, John Stone <johns_at_ks.uiuc.edu> wrote:
>
> Hi,
> The length of the trajectory shouldn't have any effect on the use
> of STRIDE, however it's quite possible that STRIDE is failing on your
> structure for some reason. Could it be that your atom coordinates
> are very large towards the end of the trajectory? (i.e. no coord
> wrapping, something like that)
>
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 18, 2005 at 02:41:02PM -0500, dimka wrote:
> > when I load a short trajectory the secondary structures are computed
> > without any problems, but when a long trajectory is loaded (700
> > frames) I get an error bellow (both at VMD startup and when I invoke
> > "mol ssrecalc top" command.)
> >
> > ERROR) Unable to find Stride output file: /tmp/fileEg7gB9
> > ERROR) Stride::read_stride_record: unable to read output file from Stride
> > ERROR) Call to Stride program failed.
> >
> > Dima
>
> --
> 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
>