VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Thu Nov 24 2011 - 08:50:40 CST

Dear VMD developers and users,

I am having a strange problem with using the stride executable with VMD
after an upgrade of the operating system from openSUSE 11.4 to openSUSE 12.1

I always used a customized stride executable that I compiled myself
because the default limits in stride.h are too stringent for my systems...
After the OS upgrade, I got errors (see below) every time I was trying
to visualize secondary structure. Before the upgrade everything worked
properly

Looking in more detail, I noticed that my stride executable is not
producing any output when run on any PDB file. For comparison, the
executable provided with VMD 1.9 is working correctly. I tried
recompiling my stride with different versions of GCC (3.3, 4.3, 4.6) but
although the compilations ran smoothly with no error, the resulting
executable was still not functional.

Has anyone seen this problem ? How was the stride_LINUXAMD64 binary
provided with VMD 1.9 compiled ? Any tricks ? I would need a stride
executable compiled with the line 43, 44 in stride.h modified as follows:

#define MAX_AT_IN_RES 500
#define MAX_AT_IN_HETERORES 500

Thank you for any suggestions

Best wishes
Vlad

My arch is x86_64 (AMD)
OS: openSUSE 12.1
VMD: 1.9 and various CVS versions, all compiled by myself (GCC 4.6) ...
(the problem is though the same is I use the distributed VMD 1.9
binaries with my stride executable)

~~~~ - 0 ( 0 ) 215 ( 215 ) 3.5
ERROR) Unable to find Stride output file: /tmp/filefxWN5v
ERROR) Stride::read_stride_record: unable to read output file from Stride
ERROR) Call to Stride program failed. 

-- 
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cellular and Developmental Biology
Roentgenstrasse 20
48149 Muenster, Germany
tel: +49-251-70365-324
fax: +49-251-70365-399
email: vlad.cojocaru[at]mpi-muenster.mpg.de