VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Nov 30 2011 - 10:24:22 CST

Vlad,
  Sorry for the delayed reply, I'm catching up on emails after being
out of the office for a few days. We don't really do anything special
when compiling the STRIDE binary that is provided along with VMD from
source code. The compilation is done using typical GCC flags for each
target platform.

Perhaps your changes to increase the residue atom count values to
500 broke something inside STRIDE?

We have modified our copy of the STRIDE source code to allow more atoms
in each residue, and to cut out some computations that
VMD doesn't want or need, and we've inserted a call to one of VMD's
fast gridsearch routines to speed up the code that finds the H-bonds.

The two most generic changes we made for our version are shown below:

% diff stride.h ../src.orig/stride.h
45,46c45
< /* #define MAX_AT_IN_RES 75 */
< #define MAX_AT_IN_RES 200 

---
> #define MAX_AT_IN_RES             75
% diff stride.c ../src.orig/stride.c
96c96
<   return(SUCCESS);
---
>   return(0);
286c286
<   Cmd->ExposedArea       = NO;
---
>   Cmd->ExposedArea       = YES;
If you like, I can send you our modified STRIDE source so you can 
play with it.
Cheers,
  John Stone
  vmd_at_ks.uiuc.edu 
On Thu, Nov 24, 2011 at 03:50:40PM +0100, Vlad Cojocaru wrote:
> 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
> 
-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078