ADL: Python] Index Error: List index out of range

Amor A. San Juan amorasj at bii.a-star.edu.sg
Tue Jan 8 19:49:10 PST 2008


Greetings,

My goal is to perform virtual screening using AutoDock4. To submit the job
to our available computing cluster, I am using the program Fullscreen
(program for virtual screening with Autodock).

During the docking process, the Fullscreen has a screening script
fullscreen.csh which calls other required scripts, including the python
scripts in Autodock. Essentially, the script uses the executable prepmol2
which showed several errors when it tries to call the several sripts in
python. The primary error message is stating that the list index is out of
range. Subsequently, all the related scripts it calls in python were also
affected and couldnt be able to run properly.

Can someone help me on this? I would greatly appreciate.

I have been also consulting with the author of Fullscreen program and
still on the progress.

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[0] 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
Abort
preparing pdbgt file from new.00001.nci.mol2
Traceback (most recent call last):
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py",
line 152, in ?
    mol = mols[0]
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/share/lib/python2.4/UserList.py",
line 28, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
setting PYTHONHOME environment
Traceback (most recent call last):
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py",
line 233, in ?
    dm.set_ligand(ligand_filename)
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py",
line 55, in set_ligand
    self.ligand = Read(ligand_filename)[0]
  File
"/HOME01/BII/biiamor/MGLTools-1.4.6/MGLToolsPckgs/MolKit/__init__.py",
line 21, in Read
-----------


Cheers,
Amor








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