ADL: python error

phil cunningham phil.cunningham at kcl.ac.uk
Thu Feb 3 03:45:29 PST 2005


Dear autodockers

I have a protein and a ligand
the protein has been processed by adt - repaired water removed and H added  saved as 1kkk.pdb
I have a ligand - starts as diz.pdb  rigid root and rotable bonds and Active tortions set saved as diz.out.pdbq
the adt viewer has 1kkk displayed and diz undisplayed (both molecules display normally)
I request Grid/Macromolecule/ChooseMacromolecule  the widget shows both 1kkk and diz I select 1kkk
python kindly informs me:-
>>> 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
at which point I am unable to procede!
Can anyone 
a) let me know what is wrong
and
b) let me know how to procede svp!

I have been throught this process 3 or 4 times all with the same outcome

1kkk is fine as I have used ito dock a different ligand successfully
before babel kindly converted to pdb diz was :-

@<TRIPOS>MOLECULE
DIZPAM10
    33    35     1
SMALL
NO_CHARGES
****
Generated from the CSD
@<TRIPOS>ATOM
     1 Cl1      4.0285    8.8762    7.3007    Cl        1 RES1      0.0000
     2 C1       3.3806    5.8970    1.2276    C.2       1 RES1      0.0000
     3 C2       4.8388    6.1400    1.5107    C.3       1 RES1      0.0000
     4 C3       5.0091    5.3001    3.7066    C.2       1 RES1      0.0000
     5 C4       5.6476    4.3680    4.6821    C.ar      1 RES1      0.0000
     6 C5       5.0824    4.0756    5.9208    C.ar      1 RES1      0.0000
     7 C6       5.7287    3.2196    6.8038    C.ar      1 RES1      0.0000
     8 C7       6.9466    2.6547    6.4648    C.ar      1 RES1      0.0000
     9 C8       7.5027    2.9325    5.2285    C.ar      1 RES1      0.0000
    10 C9       3.5802    8.0309    5.8514    C.ar      1 RES1      0.0000
    11 C10      6.8616    3.7778    4.3415    C.ar      1 RES1      0.0000
    12 C11      2.4413    8.4048    5.1662    C.ar      1 RES1      0.0000
    13 C12      2.1312    7.7545    3.9897    C.ar      1 RES1      0.0000
    14 C13      2.9393    6.7356    3.4880    C.ar      1 RES1      0.0000
    15 C14      4.0937    6.3550    4.1971    C.ar      1 RES1      0.0000
    16 C15      4.3896    7.0267    5.3840    C.ar      1 RES1      0.0000
    17 C16      1.1115    5.8449    2.0475    C.3       1 RES1      0.0000
    18 H1       4.9577    7.1335    1.8569    H         1 RES1      0.0000
    19 H2       5.3355    6.0319    0.6229    H         1 RES1      0.0000
    20 H3       4.1670    4.4588    6.1848    H         1 RES1      0.0000
    21 H4       5.3303    3.0727    7.7649    H         1 RES1      0.0000
    22 H5       7.4365    2.0645    7.1500    H         1 RES1      0.0000
    23 H6       8.3767    2.5826    4.9613    H         1 RES1      0.0000
    24 H7       7.2277    3.9861    3.4601    H         1 RES1      0.0000
    25 H8       1.8426    9.1273    5.5451    H         1 RES1      0.0000
    26 H9       1.3065    8.0349    3.5024    H         1 RES1      0.0000
    27 H10      5.2169    6.7864    5.8602    H         1 RES1      0.0000
    28 H11      0.6446    5.8009    2.9241    H         1 RES1      0.0000
    29 H12      0.7328    6.5593    1.4724    H         1 RES1      0.0000
    30 H13      0.9823    4.9916    1.5586    H         1 RES1      0.0000
    31 N1       5.3429    5.1625    2.4719    N.2       1 RES1      0.0000
    32 N2       2.5413    6.0826    2.2892    N.am      1 RES1      0.0000
    33 O1       2.9683    5.5298    0.1420    O.2       1 RES1      0.0000
@<TRIPOS>BOND
     1     1    10    1
     2     2     3    1
     3     2    32    am
     4     2    33    2
     5     3    18    1
     6     3    19    1
     7     3    31    1
     8     4     5    1
     9     4    15    1
    10     4    31    2
    11     5     6    ar
    12     5    11    ar
    13     6     7    ar
    14     6    20    1
    15     7     8    ar
    16     7    21    1
    17     8     9    ar
    18     8    22    1
    19     9    11    ar
    20     9    23    1
    21    10    12    ar
    22    10    16    ar
    23    11    24    1
    24    12    13    ar
    25    12    25    1
    26    13    14    ar
    27    13    26    1
    28    14    15    ar
    29    14    32    1
    30    15    16    ar
    31    16    27    1
    32    17    28    1
    33    17    29    1
    34    17    30    1
    35    17    32    1
@<TRIPOS>SUBSTRUCTURE
     1 RES1       1
@<TRIPOS>CRYSIN
   12.9284   13.3537    7.9763   90.0000   90.0100   90.0000    14     2
 

----------------------
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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