VMD-L Mailing List

From: Nadine Utz (nadine_at_mmb.pcb.ub.es)
Date: Fri Mar 05 2010 - 10:29:34 CST

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