[Dock-fans] sphgen error (ethel urzo)
sbrozell at rci.rutgers.edu
Tue Jun 9 13:09:44 PDT 2009
Initially, you referred to rec.ms
The error message refers to receptor.ms
Verify that your filenames are consistent.
Have you ran
Also based on an earlier thread you may need to send a Chimera
produced molecular surface of the receptor file through dos2unix.
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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