VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Mar 05 2010 - 14:46:07 CST

Hi,
  You might have a look at the STRIDE source code and see if there
is a hard-coded array size that can be easily tweaked to correct
this problem. I can send you the STRIDE source code if you want to
give it a try.

Cheers,
  John

On Fri, Mar 05, 2010 at 05:29:34PM +0100, Nadine Utz wrote:
> Dear vmd users,
>
> this is again a STRIDE problem and I am aware about the fact that STRIDE
> is not developed by vmd, but I hope that there is anybody who had the
> same problem before and might know a solution.
>
> Once in a while stride (vmd-1.8.6 as well as 1.8.7) fails to show the
> secondary structure of a protein with this error message:
>
> File /tmp/file5jqefB has too many atoms in residue G92 272
> Error reading PDB file /tmp/file5jqefB
> ERROR) Unable to find Stride output file: /tmp/fileWZXwrt
> ERROR) Stride::read_stride_record: unable to read output file from Stride
> ERROR) Call to Stride program failed.
>
> This is a problem of the organic ligand in the protein (residue 272,
> resname G92). It happens if I load amber trajectories as well as a pdb
> (--> not a problem of too large x,y,z trajectories). If I load the same
> protein with a different ligand or if I delete the ligand in the pdb
> file everything is fine. So I did a little bit trial and error and found
> out that everything is fine if the ligand has not more than 74 atoms (I
> just deleted the last atoms of the ligand in the pdb file).
>
> As I have some simulations with a ligand of 1 residue and more than 74
> atoms it would be great if
> 1. there is a way that stride works with a larger ligand
> 2. find a different solution (e.g. ligand with 2 residues ...)
>
> Thank you very much in advance and best wishes,
>
> Nadine
>
> ------------------------------------------------------------
> Dr. Nadine Utz
> Molecular Modelling & Bioinformatics Group
> Institute for Research in Biomedicine (IRB) Barcelona
> Parc Cíentific
> c/ Baldiri Reixac 10
> 08028 Barcelona
> SPAIN
> 

-- 
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