Pdbqt output missing protein side chains

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Pdbqt output missing protein side chains

David van der Spoel
Hi,

I am trying to generate pdbqt input for Autodock and friends using

obabel -ipdb 3nya.pdb -opdbqt -xrp > 3nya.pdbqt

Input for first residue:

ATOM      1  N   TRP A  32     -17.931  26.881 -57.510  1.00 84.68
     N
ATOM      2  CA  TRP A  32     -18.091  25.544 -56.851  1.00 84.93
     C
ATOM      3  C   TRP A  32     -16.738  24.885 -56.582  1.00 84.23
     C
ATOM      4  O   TRP A  32     -16.579  24.154 -55.599  1.00 84.28
     O
ATOM      5  CB  TRP A  32     -18.957  24.606 -57.705  1.00 85.29
     C
ATOM      6  CG  TRP A  32     -19.361  23.324 -56.991  1.00 86.80
     C
ATOM      7  CD1 TRP A  32     -20.497  23.118 -56.256  1.00 87.70
     C
ATOM      8  CD2 TRP A  32     -18.628  22.079 -56.957  1.00 88.63
     C
ATOM      9  NE1 TRP A  32     -20.518  21.828 -55.767  1.00 88.97
     N
ATOM     10  CE2 TRP A  32     -19.386  21.169 -56.179  1.00 89.35
     C
ATOM     11  CE3 TRP A  32     -17.405  21.648 -57.505  1.00 88.78
     C
ATOM     12  CZ2 TRP A  32     -18.959  19.845 -55.933  1.00 89.38
     C
ATOM     13  CZ3 TRP A  32     -16.981  20.330 -57.261  1.00 88.90
     C
ATOM     14  CH2 TRP A  32     -17.759  19.449 -56.482  1.00 89.12
     C
ATOM     15  N   VAL A  33     -15.779  25.125 -57.472  1.00 83.39
     N

Output:

ATOM      1  N   TRP A   1     -17.931  26.881 -57.510  0.00  0.00
-0.123 NA
ATOM      2  CA  TRP A   1     -18.091  25.544 -56.851  0.00  0.00
+0.174 C
ATOM      3  C   TRP A   1     -16.738  24.885 -56.582  0.00  0.00
+0.260 C
ATOM      4  O   TRP A   1     -16.579  24.154 -55.599  0.00  0.00
-0.272 OA
ATOM      5  N   VAL A   2     -15.779  25.125 -57.472  0.00  0.00
-0.197 NA

The Side chain is gone!
Any clues?
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se

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