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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