VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Jan 25 2008 - 00:17:48 CST

Hi,
  You'll have to ask the author of the Timeline plugin about the
diagnostic messages its outputting, but most of them look harmless.
The one message that indicates a problem is the ERROR) message from
STRIDE, which is the program that determines secondary structure.
For some reason STRIDE is failing to calculate the secondary structure
for one of your timesteps. Do the various "cartoon" representations
work correctly on your machine? If not, then there may be some issue
with STRIDE and your structure. If it does work, then STRIDE may have
a problem with one particular frame in your trajectory.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Jan 25, 2008 at 11:42:17AM +0530, aneesh cna wrote:
> Hello VMD users,
> I am try to use the Timeline plug in in the VMD for time
> evaluation of secondary structure for a small stretch of residue ( 5-10 nos)
> in my protein. But when i am selecting the ' calc.sec.stru ' option in
> timeline plug in it showing errors as follows in the console even though it
> runing.
> last data name at 354
> set frame to 351
> now update for mol 0
> updated
> last data name at 355
> set frame to 352
> now update for mol 0
> No hydrogen bonds found in /usr/tmp/file7el8ux
> ERROR) Unable to find Stride output file: /usr/tmp/filejN2rPG
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
> updated
> last data name at 356
> set frame to 353
> now update for mol 0
> updated
> last data name at 357
> set frame to 354
>
> what could be the reason ?.
>
> Thanks in Advance
>
> Regards
> Aneesh 

-- 
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