Dear OpenBabel mailing list, I'm using OpenBabel 3.1.1 and the Python to C++ bindings to load pdbqt files and convert them to pdb with explicit hydrogens. Unfortunately, I can't add nonpolar hydrogens using OpenBabel. I can do this using Autodock's PMV GUI as a test and comparison, so my concern is not the underlying molecule.
In the python bindings, I've tried combinations of AddHydrogens(), AddNewHydrogens(), AddPolarHydrogens(), AddNonPolarHydrogens(), checking the OBMol.NumAtoms() each time, and nothing changes. In the OpenBabel GUI I've loaded the pdbqt files and tried combinations of "Add hydrogens (make explicit)", "Add hydrogens to nonpolar atoms only", and "Adds hydrogens to polar atoms only". Nothing changes the pdb output. Note: There is one polar-hydrogen present which can be removed and added back. Ultimately, I must determine why the Python bindings aren't adding hydrogens. Using the GUI was a sanity check. I've included for you below a copy & paste of a pdbqt file. Many thanks for your help. REMARK VINA RESULT: -8.009 0.000 0.000 REMARK INTER + INTRA: -11.923 REMARK INTER: -10.819 REMARK INTRA: -1.105 REMARK UNBOUND: -1.105 REMARK Name = ZINC000004125379 REMARK x y z vdW Elec q Type REMARK _______ _______ _______ _____ _____ ______ ____ ROOT ATOM 1 C LIG 1 -7.551 101.695 50.079 0.00 0.00 -0.030 A ATOM 2 C LIG 1 -7.837 101.486 48.730 0.00 0.00 +0.090 A ATOM 3 C LIG 1 -9.147 101.402 48.306 0.00 0.00 +0.030 A ATOM 4 C LIG 1 -10.180 101.524 49.216 0.00 0.00 -0.050 A ATOM 5 C LIG 1 -9.907 101.732 50.562 0.00 0.00 +0.130 A ATOM 6 C LIG 1 -11.610 101.431 48.746 0.00 0.00 +0.100 C ATOM 7 C LIG 1 -8.592 101.813 50.998 0.00 0.00 +0.120 A ENDROOT BRANCH 1 13 ATOM 8 C LIG 1 -3.446 102.767 52.833 0.00 0.00 +0.240 A ATOM 9 N LIG 1 -2.257 102.405 52.445 0.00 0.00 -0.250 NA ATOM 10 N LIG 1 -2.330 101.778 51.323 0.00 0.00 -0.230 NA ATOM 11 C LIG 1 -3.581 101.712 50.944 0.00 0.00 +0.080 A ATOM 12 S LIG 1 -4.712 101.147 49.709 0.00 0.00 +0.190 S ATOM 13 C LIG 1 -6.145 101.786 50.535 0.00 0.00 +0.170 A ATOM 14 N LIG 1 -5.709 102.349 51.619 0.00 0.00 -0.250 NA ATOM 15 N LIG 1 -4.348 102.331 51.887 0.00 0.00 -0.340 N BRANCH 8 17 ATOM 16 C LIG 1 -3.372 102.687 55.311 0.00 0.00 +0.060 C ATOM 17 C LIG 1 -3.777 103.522 54.095 0.00 0.00 +0.160 C ENDBRANCH 8 17 ENDBRANCH 1 13 BRANCH 5 18 ATOM 18 N LIG 1 -10.956 101.853 51.480 0.00 0.00 -0.620 N ATOM 19 H LIG 1 -11.561 102.610 51.427 0.00 0.00 +0.410 HD BRANCH 18 20 ATOM 20 C LIG 1 -11.124 100.921 52.438 0.00 0.00 +0.510 C ATOM 21 S LIG 1 -10.962 99.261 52.056 0.00 0.00 -0.470 S BRANCH 20 22 ATOM 22 N LIG 1 -11.419 101.297 53.699 0.00 0.00 -0.640 N ATOM 23 H LIG 1 -12.344 101.330 53.991 0.00 0.00 +0.410 HD ATOM 24 C LIG 1 -10.431 101.629 54.553 0.00 0.00 +0.530 C ATOM 25 O LIG 1 -9.272 101.589 54.186 0.00 0.00 -0.380 OA BRANCH 24 26 ATOM 26 C LIG 1 -10.754 102.041 55.932 0.00 0.00 -0.180 A ATOM 27 C LIG 1 -10.619 103.376 56.316 0.00 0.00 +0.070 A ATOM 28 C LIG 1 -10.922 103.754 57.607 0.00 0.00 +0.000 A ATOM 29 C LIG 1 -11.361 102.814 58.524 0.00 0.00 +0.080 A ATOM 30 C LIG 1 -11.500 101.489 58.153 0.00 0.00 -0.010 A ATOM 31 C LIG 1 -11.205 101.095 56.861 0.00 0.00 +0.170 A ATOM 32 F LIG 1 -11.341 99.801 56.499 0.00 0.00 -0.110 F ENDBRANCH 24 26 ENDBRANCH 20 22 ENDBRANCH 18 20 ENDBRANCH 5 18 TORSDOF 6 *Dr Anthony Nash PhD MRSC MSc MSc BSc* Computational Chemistry Consultant Warwick, United Kingdom
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