ADL: error while converting ligand files from .pdb to .pdbqt

Ксения Сафина cat7mail.ru at mail.ru
Fri Mar 7 08:31:21 PST 2014


 Hi Rob,

I've faced the same problem with oligosaccharide. Distances between some atoms in my structure were about 1.6 A, and Autodock didn't recognize any kind of bond between them. You can open your structure in ADT to see two single residues.
I've used 'obminimize' tool from OpenBabel toolbox with small number of steps. My structure was suitable for prepare_ligand4.py script after 100 steps (default is 2500).


>Hi Stefano et al,
>
>I tried a lot of things but can't get my head around why prepare_ligand4.py
>sees this peptide ligand  as a split one (see below warning) and therefore
>writes only a partial PDBQT. For some reason it insists there is a cut
>between the first (N-terminal) residue's peptide bond C atom and the
>following N of the second residue, so between PHE and LEU in the attached
>ligand PDB file.
>
>WARNING: 14 atoms of 59 in ligands/1JQ9_FH_ligand.pdb were not written  [I
>used the -F switch]
>
>I've tried to circle in on the problem by deleting all PHE atoms apart from
>N, Ca and C, and also keeping only the two first residues PHE and LEU in the
>file (as done below), but the problem remains. Maybe it's obvious but I
>can't see it. Is there any docu on how the script decides such things?
>
>Thanks a lot,
>Rob
>
>---
>
>ATOM      1  N   PHE P   1       8.575  15.709  38.306  1.00 43.28 
>N 
>ATOM      2  CA  PHE P   1       9.602  15.861  37.235  1.00 41.57 
>C 
>ATOM      3  C   PHE P   1       9.830  17.345  36.978  1.00 42.69 
>C 
>ATOM      4  O   PHE P   1       9.803  17.772  35.824  1.00 43.50 
>O 
>ATOM      5  CB  PHE P   1       9.117  15.215  35.933  1.00 35.06 
>C 
>ATOM      6  CG  PHE P   1       8.092  14.134  36.131  1.00 31.19 
>C 
>ATOM      7  CD1 PHE P   1       8.428  12.940  36.760  1.00 39.51 
>C 
>ATOM      8  CD2 PHE P   1       6.780  14.317  35.700  1.00 39.51 
>C 
>ATOM      9  CE1 PHE P   1       7.473  11.944  36.959  1.00 39.01 
>C 
>ATOM     10  CE2 PHE P   1       5.818  13.328  35.896  1.00 39.01 
>C 
>ATOM     11  CZ  PHE P   1       6.164  12.139  36.526  1.00 38.87 
>C 
>ATOM     12  HA  PHE P   1      10.422  15.429  37.523  1.00 41.57 
>H 
>ATOM     13  HB2 PHE P   1       8.741  15.903  35.362  1.00 35.06 
>H 
>ATOM     14  HB3 PHE P   1       9.880  14.842  35.464  1.00 35.06 
>H 
>ATOM     15  HD1 PHE P   1       9.301  12.804  37.052  1.00 39.51 
>H 
>ATOM     16  HD2 PHE P   1       6.543  15.110  35.276  1.00 39.51 
>H 
>ATOM     17  HE1 PHE P   1       7.710  11.150  37.381  1.00 39.01 
>H 
>ATOM     18  HE2 PHE P   1       4.945  13.464  35.605  1.00 39.01 
>H 
>ATOM     19  HZ  PHE P   1       5.525  11.477  36.658  1.00 38.87 
>H 
>ATOM     20  H1  PHE P   1       8.771  15.000  38.807  1.00 43.28 
>H 
>ATOM     21  H2  PHE P   1       8.567  16.438  38.816  1.00 43.28 
>H 
>ATOM     22  H3  PHE P   1       7.773  15.598  37.935  1.00 43.28 
>H 
>ATOM     23  N   LEU P   2      10.114  17.764  38.535  1.00 42.45 
>N 
>ATOM     24  CA  LEU P   2      10.318  19.205  38.410  1.00 41.07 
>C 
>ATOM     25  C   LEU P   2      10.795  20.058  39.586  1.00 31.93 
>C 
>ATOM     26  O   LEU P   2      10.339  21.190  39.731  1.00 32.53 
>O 
>ATOM     27  CB  LEU P   2       9.034  19.843  37.873  1.00 36.43 
>C 
>ATOM     28  CG  LEU P   2       7.640  19.500  38.429  1.00 34.11 
>C 
>ATOM     29  CD1 LEU P   2       7.216  18.103  38.004  1.00 33.27 
>C 
>ATOM     30  CD2 LEU P   2       7.640  19.616  39.925  1.00 26.81 
>C 
>ATOM     31  H   LEU P   2      10.153  17.333  39.278  1.00 42.45 
>H 
>ATOM     32  HA  LEU P   2      11.092  19.219  37.825  1.00 41.07 
>H 
>ATOM     33  HB2 LEU P   2       9.141  20.802  37.968  1.00 36.43 
>H 
>ATOM     34  HB3 LEU P   2       9.007  19.653  36.922  1.00 36.43 
>H 
>ATOM     35  HG  LEU P   2       7.000  20.132  38.065  1.00 34.11 
>H 
>ATOM     36 HD11 LEU P   2       6.337  17.908  38.364  1.00 33.27 
>H 
>ATOM     37 HD12 LEU P   2       7.186  18.054  37.036  1.00 33.27 
>H 
>ATOM     38 HD13 LEU P   2       7.854  17.455  38.340  1.00 33.27 
>H 
>ATOM     39 HD21 LEU P   2       6.759  19.398  40.267  1.00 26.81 
>H 
>ATOM     40 HD22 LEU P   2       8.292  19.001  40.297  1.00 26.81 
>H 
>ATOM     41 HD23 LEU P   2       7.870  20.523  40.179  1.00 26.81 
>H 
>
>
>

Hope this helps,
Ksenia 


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