ADL: Error loading AutoDock Tools

Sargis Dallakyan sargis at scripps.edu
Mon Jun 22 15:44:05 PDT 2009


venkat wrote:
> Hi 
> I am trying to run prepare_ligand, I got following error message in between
> 
> 
> 00284.nci_2.mol2
> setting PYTHONHOME environment
> Traceback (most recent call last):
>   File "prepare_ligand4.py", line 153, in <module>
>     mols = Read(ligand_filename)
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/__init__.py", line 51, in Read
>     molecules = parser.parse()
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/mol2Parser.py", line 118, in parse
>     self.build4LevelsTree({},atmlines)
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/mol2Parser.py", line 372, in build4LevelsTree
>     res = self.mol.curChain.get( na )
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 1264, in get
>     return self.children.get(function)
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 612, in get
>     escapeCharacters=escapeCharacters)
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 162, in select
>     newNodes = self.processListItem(nodes, item, sets)
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/protein.py", line 399, in processListItem
>     return TreeNodeSetSelector.processListItem(self, nodes, item, sets=sets)
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/tree.py", line 217, in processListItem
>     newNodes = self.getRange( nodes, item )
>   File "/home/vk/pgm/mgltools_x86_64Linux2_1.5.4/MGLToolsPckgs/MolKit/protein.py", line 352, in getRange
>     if levItList[0][0]=='#' and levItList[1][0]=='#':
> IndexError: string index out of range
> 00285.nci_2.mol2
> setting PYTHONHOME environment
> 00286.nci_2.mol2

I can try to reproduce this bug if I can access 00285.nci_2.mol2. Please 
use one of the two methods described here to submit this file:
http://mgltools.scripps.edu/documentation/how-to/report-a-bug

Thank you,
Sargis


-- 

Sargis Dallakyan, Ph.D. - Research Programmer III
The Scripps Research Institute,
Dept. Molecular Biology,  MB-5,
10550  North Torrey Pines Road,
La Jolla,  CA 92037-1000
Tel: (858) 784-9559
http://mgltools.scripps.edu/Members/sargis


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