Sorry - I saw that no one responded. I haven't used the PBQT format myself, but:
r Output as a rigid molecule (i.e. no branches or torsion tree)
So my guess is that the -xr is removing the side chain perhaps?
-Geoff
> On Aug 2, 2017, at 4:14 AM, David van der Spoel <sp...@xray.bmc.uu.se> wrote:
>
> 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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