ADL: python error again!

phil cunningham phil.cunningham at kcl.ac.uk
Thu Jan 12 06:25:31 PST 2006


Dear Autodockers

I have a protein xxx.pdb - 'repaired' and polar H added by ADT



as soon as I request the the grid menu to read this file it 'bombs out' 
with the follow message
>>> 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



can anyone decipher the message ?  which index out of range?

I have checked the pdb layout and it looks fine to me
         1         2         3         4         5         6         7
1234567890123456789012345678901234567890123456789012345678901234567890
ATOM      1  N   TYR A   2      48.015  88.294 142.309  0.00  0.00           N  
ATOM      2  HN  TYR A   2      47.417  89.022 141.918  1.00  0.00           H  
ATOM      3  CA  TYR A   2      47.426  87.037 141.828  0.00  0.00           C  
ATOM      4  C   TYR A   2      47.582  85.869 142.813  0.00  0.00           C  
ATOM      5  O   TYR A   2      46.773  84.940 142.793  0.00  0.00           O  
ATOM      6  CB  TYR A   2      47.972  86.667 140.436  0.00  0.00           C  
ATOM      7  CG  TYR A   2      49.244  85.855 140.413  0.00  0.00           C  
ATOM      8  CD1 TYR A   2      49.222  84.491 140.733  0.00  0.00           C  
ATOM      9  CD2 TYR A   2      50.471  86.438 140.027  0.00  0.00           C  
ATOM     10  CE1 TYR A   2      50.380  83.718 140.670  0.00  0.00           C


does the residue sequence number have to start at 1? (col 26 above)
hope someone can assist
phil

----------------------
Phil Cunningham
Senior Bioinformatics Officer
King's College London
Franklin Wilkins Building
150 Stamford Street
SE1 9NH
London SE1 9NN
tel 020 7848 4239
fax 020 7848 4500
email phil.cunningham at kcl.ac.uk




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