ADL: bug or user error?

Phil Cunningham phil.cunningham at kcl.ac.uk
Thu Jun 25 06:54:17 PDT 2009


Using Autodock 3  and ADT
source file from PDB (EBI)
load repair module / repair missing atoms (non)
edit charges / compute gasteiger /check totals /spread on all atoms
edit hydrogens / add / polar only  /
save / write PDB

load via ligand / input molecule / read molecule

get a red python screen full saying:-

more py_err
Python 2.3.2 (#6, Dec 11 2003, 15:11:30)
[GCC 2.95.3 20010315 (SuSE)] on linux2
Type "copyright", "credits" or "license()" for more information.

    ****************************************************************
    Personal firewall software may warn about the connection IDLE
    makes to its subprocess using this computer's internal loopback
    interface.  This connection is not visible on any external
    interface and no data is sent to or received from the Internet.
    ****************************************************************
   
IDLE 1.0      ==== No Subprocess ====
 >>> ERROR ************************************************
Traceback (most recent call last):
  File 
"/data/people/stqp7486/progs/autod/share/lib/python2.3/site-packages/ViewerFramework/VF.py", 
line 582, in tryto
    result = apply( command, args, kw )
  File 
"/data/people/stqp7486/progs/autod/share/lib/python2.3/site-packages/AutoDockTools/autogpfCommands.py", 
line 455, in doit
    nphs = mol.allAtoms.get(lambda x: x.element=='H' and \
  File 
"/data/people/stqp7486/progs/autod/share/lib/python2.3/site-packages/MolKit/tree.py", 
line 157, in get
    return self.ReturnType(filter(who, self.data))
  File 
"/data/people/stqp7486/progs/autod/share/lib/python2.3/site-packages/AutoDockTools/autogpfCommands.py", 
line 455, in <lambda>
    nphs = mol.allAtoms.get(lambda x: x.element=='H' and \
  File 
"/data/people/stqp7486/progs/autod/share/lib/python2.3/UserList.py", 
line 28, in __getitem__
    def __getitem__(self, i): return self.data[i]
IndexError: list index out of range


anybody know what is going on?

Phil

-- 
Phil Cunningham
Senior Bioinformatics Officer
Room 3.157 Franklin Wilkins Building
Department of Biochemistry
King's College University of London
150 Stanford Street
London SE1 9NH

tel 020 7848 4239
fax 020 7848 4500

email phil.cunningham at kcl.ac.uk



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