[Dock-fans] bash:sphgen: command not found (Again!)

John J. Irwin jji at cgl.ucsf.edu
Thu Apr 24 11:06:13 PDT 2008

Hi Carlo

You need to be in the directory where the INSPH is located, and 
reference sphgen, or add its directory to your path.

Thus, in the directory with INSPH, type



(in c-shell)
set path = ($path /usr/local/dock6/bin)
in directory with SPHGEN:


Good luck!


Carlo Zambonelli wrote:
> Dear Dock-fans,
> I am new to cygwin, to linux and to Dock, so please be patient and if
> necessary redirect me to "required readings" in addition to anything I
> can find on the Dock web page, which I already read.
> I successfully installed Cygwin, Dock6.2 and DMS. I completed the
> tutorial Structure Preparation and I am working on the tutorial Sphere
> Generation and Selection. I ran DMS successfully and now I have rec.ms
> and INSPH in my working directory. When I run sphgen I obtain the
> following error:
> bash: sphgen: command not found
> sphgen.exe is located in directory /usr/local/dock6/bin. If I run sphgen
> from this directory I obtain the following message:
> open: No such file or directory
> apparent state: unit 5 named INSPH
> lately writing direct unformatted external IO
> Segmentation fault (core dumped)
> The first line correctly tells me that I do not have the INSPH file in
> this directory. What is the meaning of the remaining of the message? It
> looks like I can not launch sphgen from my working directory, as I
> expected. When I ran DMS from the same working directory everything went
> smoothly.
> I read all the threads dealing with this problem at no avail: I tried to
> make the sphgen.exe executable with the command
> chmod 755 sphgen
> For sake of completeness of information:
> -- sphgen is located in the following directory:
> usr/local/Dock6/bin
> -- DMS is located in:
> usr/local/dms
> -- my working directory is:
> /usr/local/dock6/tutorials/struct_prep
> Any help would be greatly appreciated!
> Carlo
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> Dock-fans at docking.org
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