ADL: summarize_results4.py

Holly Freedman freedman at phys.ualberta.ca
Tue Jan 15 17:10:53 PST 2008


Jack,
Yes, I am running on Mac Intel.  I can get as far as displaying the help - I think the problem is the 
size of my directory.  Maybe I should try on Linux.
Holly

> 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 summarize_results4.py 
> 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: summarize_results4.py -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 scripps.edu on behalf of Holly Freedman
> Sent: Tue 1/15/2008 7:19 PM
> To: autodock at scripps.edu
> Subject: Re: ADL: summarize_results4.py
>  
> 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
> 
> > 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 scripps.edu [mailto:autodock-bounces at scripps.edu]
> > On Behalf Of Holly Freedman
> > Sent: Tuesday, January 15, 2008 5:26 PM
> > To: autodock at scripps.edu
> > Subject: ADL: summarize_results4.py
> > 
> > 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
> > 
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> > 
> > ________________________________________________
> > --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> 
> --
> Department of Physics, University of Alberta
> Edmonton CANADA
> 
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
> 
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---



--
Department of Physics, University of Alberta
Edmonton CANADA



More information about the autodock mailing list