Holly Freedman freedman at
Tue Jan 15 16:19:46 PST 2008

Hi Jack,

Yes, it seems to start to work if I run with pythonsh as you described.  I am still getting stuck, but I 
think it is a memory problem this time:

python(25999) malloc: *** vm_allocate(size=411045888) failed (error code=3)
python(25999) malloc: *** error: can't allocate region
python(25999) malloc: *** set a breakpoint in szone_error to debug
Bus error

Thanks for your help with pythonsh,

> Holly,
> I do things a little differently since I run my simulations on a
> distributed project so I've ported the python scripts to binaries. I
> have to check if this will work when I get home. But this is the command
> line I am using currently
> summarize_results4 -d . -r receptor_file.pdbqt -o summary.txt 
> You may need to run it with
> pythonsh summarize_results4 -d . -r receptor_file.pdbqt -o summary.txt
> If you don't have pythonsh in your $PATH then that won't work, you may
> need to fix some of your configuration.
> Jack
> -----Original Message-----
> From: autodock-bounces at [mailto:autodock-bounces at]
> On Behalf Of Holly Freedman
> Sent: Tuesday, January 15, 2008 5:26 PM
> To: autodock at
> Subject: ADL:
> Dear Jack Shultz and  Arneh Babakhani,
> Thank you for your suggestions.  I'm not sure how to set my AD and MGL
> environmental variables.  I 
> have run ADT on the Mac but no other AD python script.  How would I run
> with pythonsh?  I tried this 
> but I wasn't sure how to do it.
> Thanks again,
> Holly Freedman
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
> ________________________________________________
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Department of Physics, University of Alberta
Edmonton CANADA

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