Hi, I'm currently struggling with the obabel software (version 2.3.90) when I use it to convert pdb files of ligands into mol2 files and adding hydrogens to a docking pose (hydrogens are implicit during the docking process). My problem is the hydrogens added tend to break aromaticity in aromatic rings and, more specifically, into pyrimidine-alike rings. The geometry of the added hydrogens are not realistic.
I have included two files (try.pdb which is converted in try.mol2 using the following command line : "obabel -ipdb try.pdb -omol2 -O try2.mol2 -p 7.0" and the same result is produced using "obabel -ipdb try.pdb -omol2 -O try2.mol2 -h") showing the current problem. If you look closely at try.mol2, a hydrogen is placed on the C4 atom and three hydrogen are added on the N3 atom forming a NH3 instead of having a single NH2 bonded to C4. The real 3D structure of the ligand (before rendering hydrogens implicit) is shown in ZINC01244402.mol2 file which has been download from http://zinc.docking.org/substance/1244402 in mol2 format. Prior to version 2.3.90, I was using version 2.3.2 of OpenBabel and the addition of hydrogens on ligands was way more unreliable than it is in the current version. I saw a major upgrade with the current version, but still cannot rely on it for realistic chemical 3D structures. Any idea how it could be improved or fixed ? Kind regards, Louis-Philippe Morency Étudiant à la Maîtrise Laboratoire du Pr Rafael Najmanovich Faculté de Médecine et des Sciences de la Santé (FMSS) Université de Sherbrooke louis-philippe.more...@usherbrooke.ca<mailto:louis-philippe.more...@usherbrooke.ca>
try.pdb
Description: try.pdb
try.mol2
Description: try.mol2
ZINC01244402.mol2
Description: ZINC01244402.mol2
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