ADL: could someone pls help me

Ruth Huey rhuey at scripps.edu
Thu Mar 27 08:06:28 PDT 2008


Hi,

There is a bug in the version of 
MGLToolsPckgs/MolKit/interactionDescriptor.py which you are using.  
Specifically, in the case where the ligand has no atoms which can 
hydrogen bond, a variable 'lig_hb_ats'  is used without being 
initialized.  This causes the error.

The bug has been fixed and the corrected file has been checked into cvs, 
the version control system we use.

IN PRINCIPLE, you can correct this by invoking 'cvs update' on the file. 
To see whether your environment supports this, type the following lines 
at your shell prompt:

cd /usr/local/MGLTools-1.4.6/MGLToolsPckgs/MolKit
cvs status interactionDescriptor.py


IF you then see this line:
===================================================================
File: interactionDescriptor.py        Status: Needs Patch

you can use cvs update the file to correct this problem:

cvs update interactionDescriptor.py


OTHERWISE, you can replace the file with the attached version of 
interactionDescriptor.py
To do that, save the attached file somewhere as  
yourpath/interactionDescriptor.py. Then

cd /usr/local/MGLTools-1.4.6/MGLToolsPckgs/MolKit
mv interactionDescriptor.py old_interactionDescriptor.py
cp yourpath/interactionDescriptor.py interactionDescriptor.py

Thank you for your interest in our tools and for your patience....

      Ruth



namita at ncbs.res.in wrote:
> hi all
> i think i have posted this query before too. i found the same doubt in tha
> mailing list archives too but not a solution for it.
> I have been trying to dock a cytochrome P450 model with a fatty acid
> ligand. Till the docking part i get no errors but once its done and i try
> to view the results i get a couple of errors.
>
> Traceback (most recent call last):
>   File "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/ViewerFramework/VF.py",
> line 714, in tryto
>     result = apply( command, args, kw )
>   File
> "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py",
> line 1922, in doit
>     self.build()
>   File
> "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py",
> line 1759, in build
>     self.intDescr = InteractionDescriptor(lig, macro, percentCutoff)
>   File
> "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/MolKit/interactionDescriptor.py",
> line 44, in __init__
>     self.build(detect_pi=detect_pi)
>   File
> "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/MolKit/interactionDescriptor.py",
> line 51, in build
>     self.buildHydrogenBonds()           #
>   File
> "/usr/local/MGLTools-1.4.6/MGLToolsPckgs/MolKit/interactionDescriptor.py",
> line 117, in buildHydrogenBonds
>     lig_gly_res = d['lig_hb_gly_res'] = lig_hb_res.get(lambda x:
> x.type=='GLY')
> UnboundLocalError: local variable 'lig_hb_res' referenced before assignment
>
> I have tried changing the grid specifications and many other parameters
> but cant find a solution to this problem.
>
> any help would be greatly appreciated.
>
> thanks
> namitha
>
> ________________________________________________
> --- ADL: AutoDock List  --- http://autodock.scripps.edu/mailing_list ---
>
>   

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