Hi David,
I just noticed this question, I've missed it too.
I've tried with your test and I've noticed that the residue is in fact there, but some
renumbering occurs (no idea why):
$ obabel -ipdb 3nya.pdb -opdbqt -xrp > 3nya.pdbqt
1 molecule converted
$ grep "TRP A 1" 3nya.pdbqt
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 3518 CB TRP A 1 -18.957 24.606 -57.705 0.00 0.00 +0.056 C
ATOM 3519 CG TRP A 1 -19.361 23.324 -56.991 0.00 0.00 +0.000 A
ATOM 3520 CD1 TRP A 1 -20.497 23.118 -56.256 0.00 0.00 +0.095 A
ATOM 3521 NE1 TRP A 1 -20.518 21.828 -55.767 0.00 0.00 -0.244 NA
ATOM 3522 CE2 TRP A 1 -19.386 21.169 -56.179 0.00 0.00 +0.081 A
ATOM 3523 CZ2 TRP A 1 -18.959 19.845 -55.933 0.00 0.00 +0.019 A
ATOM 3524 CH2 TRP A 1 -17.759 19.449 -56.482 0.00 0.00 +0.002 A
ATOM 3525 CZ3 TRP A 1 -16.981 20.330 -57.261 0.00 0.00 +0.000 A
ATOM 3526 CE3 TRP A 1 -17.405 21.648 -57.505 0.00 0.00 +0.001 A
ATOM 3527 CD2 TRP A 1 -18.628 22.079 -56.957 0.00 0.00 +0.015 A
I'm not sure where that comes from, but it shouldn't be a problem for your dockings. If
you use Vina, you have to clean up the PDBQT to remove flexibility specifications
(ROOT/ENDROOT lines) as well as removing waters and ligands, which OB nicely prepares for
you as flexible.
The OB PDBQT format misses an option to specify that you're preparing a receptor, to
prevent writing the flexibility lines above. The '-xr' option basically defines a single,
huge rigid body in between root/endroot specifications (I know, it's messy, but we're
working on it...).
Let me know if you have any problems.
S
On 08/16/2017 01:09 PM, Geoffrey Hutchison wrote:
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
<mailto: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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--
Stefano Forli, PhD
Assistant Professor
Dept. of Integrative Structural
and Computational Biology, MB-112A
The Scripps Research Institute
10550 North Torrey Pines Road
La Jolla, CA 92037-1000, USA.
tel: +1 (858)784-2055
fax: +1 (858)784-2860
email: fo...@scripps.edu
http://www.scripps.edu/~forli/
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