ADL: Python] Index Error: List index out of range
sargis at scripps.edu
Wed Jan 9 10:09:04 PST 2008
> Since the error flag list index out of range means that the script tries
> to access an element which is out in the list, I have checked the input
> ligand file '00001.nci.mol2' and it seems sensible with gasteiger charges
> and in Tripos mol2 format.
> I also checked the python script prepare_ligand4.py and the line 152 with
> 'mol=mols is causing mismatch or perhaps incompatibilities with the
> script prepmol2.
> Below is the error flag:
> /HOME01/BII/biiamor/2007/AD/i86Linux2/autogrid4: Successful Completion.
> ls: No match.
> Trying file 00001.nci.mol2
> Processing No 1 ligand 00001
> invalid number: incomprehensible list input
> apparent state: internal I/O
> lately reading sequential formatted internal IO
> Prepmol2: file 00001.nci.mol2 opened OK
> Prepmol2: file 00001.nci.mol2.new opened OK
> preparing pdbgt file from new.00001.nci.mol2
> Traceback (most recent call last):
> line 152, in ?
> mol = mols
> line 28, in __getitem__
> def __getitem__(self, i): return self.data[i]
> IndexError: list index out of range
prepare_ligand4.py checks if the input file exists, but if its empty or has no
molecule in it, then mols is an empty list () which can lead to this error.
You wrote that you checked 00001.nci.mol2, but it seems that new.00001.nci.mol2
is passed to prepare_ligand4.py. Add -v option to prepare_ligand4.py to get
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