Shultz, Jack JShultz at
Tue Jan 15 16:46:33 PST 2008

Reminds me of the error I got when I tried porting these python scripts to a binary on Mac Intel. I had malloc errors. Are you porting to Mac Intel? I recall being able to at least run them on Mac Intel. 

Are you able to at least run this?

m-mac207722:/Library/MGLTools/1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24 jshultz$ pythonsh 
Starting X11
2008-01-15 19:45:56.281 open[19520] Couldn't launch application:  X11
setting PYTHONHOME environment
summarize_results4: directory must be specified.
Usage: -d directory

    Description of command...
         -d     directory
    Optional parameters:
        [-t]    rmsd tolerance (default is 1.0)
        [-f]    rmsd reference filename 
        (default is to use input ligand coordinates from docking log)
        [-b]    print best docking info only (default is print all)
        [-L]    print largest cluster info only (default is print all)
        [-B]    print best docking and largest cluster info only (default is print all)
        [-o]    output filename
                      (default is 'summary_of_results')
        [-a]    append to  output filename
                      (default is to open output filename 'w')
        [-k]    build hydrogen bonds and report number built
        [-e]    compute estat, vdw, hb + desolv energies and report breakdown
        [-r]    receptor filename
        [-u]    report unbound energy
        [-v]    verbose output

-----Original Message-----
From: autodock-bounces at on behalf of Holly Freedman
Sent: Tue 1/15/2008 7:19 PM
To: autodock at
Subject: Re: ADL:
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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> ________________________________________________
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Department of Physics, University of Alberta
Edmonton CANADA

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