[Dock-fans] sphgen error (ethel urzo)

Scott Brozell sbrozell at rci.rutgers.edu
Tue Jun 9 13:09:44 PDT 2009


Hi,

Initially, you referred to rec.ms 
The error message refers to receptor.ms
Verify that your filenames are consistent.
Have you ran 
http://dock.compbio.ucsf.edu/DOCK_6/tutorials/sphere_generation/generating_spheres.htm
?
Also based on an earlier thread you may need to send a Chimera
produced molecular surface of the receptor file through dos2unix.

Scott

On Fri, Jun 05, 2009 at 05:24:47PM -0700, ethel urzo wrote:
> I tried making the INSPH file using Etext Editor (Unix-like text editor).
> But I got the ff error:
> 
> $ sphgen
> open: No such file or directory
> apparent state: unit 4 named receptor.ms
> lately reading sequential formatted external IO
>       6 [sig] sphgen 3536 _cygtls::handle_exceptions: Error while dumping state
> (probably corrupted stack)
> Segmentation fault (core dumped)
> 
> I think we have resolved the error on INSPH and now it's about receptor.ms.
> I prepared this .ms file using Chimera.
> I've also tried changing it as .dms,
> 
> --- On Sat, 6/6/09, Ben Keshet <keshet1 at umbc.edu> wrote:
> 
> How did you create the INSPH file?  I think the file should be just 
> INSPH, and not INSPH.txt.  Try creating the file using a simple 
> unix-like text editor, like pico or nano, and save the file only as 
> INSPH (CTRL+o).  Also, before running sphgen, make sure you delete any 
> error files that you may have created in previous failed runs.
> 
> > Date: Fri, 5 Jun 2009 07:03:06 -0700 (PDT)
> > From: ethel urzo <reau_05 at yahoo.com>
> > I've already have the rec.ms file and INSPH.txt in the folder containing sphgen.exe...
> > When I run the command sphgen, I got the following error:
> >
> > open: No such file or directory
> > apparent state: unit 5 named INSPH
> > lately writing direct unformatted external IO
> > ????? 6 [sig] sphgen 2564 _cygtls::handle_exceptions: Error while dumping state
> > (probably corrupted stack)
> > Segmentation fault (core dumped)
> > and then a file named sphgen.exe.stackdump appeared.


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