Any particular reason you are using PDB files to store chemical structures? PDB files don't contain bond order information, so Open Babel has to guess it. If you just stored the structure in MOL2 or MOL, with the correct bond orders, you wouldn't have this problem.
- Noel On 22 August 2013 22:07, Morency, Louis-Philippe <louis-philippe.more...@usherbrooke.ca> wrote: > 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 > > > > ------------------------------------------------------------------------------ > Introducing Performance Central, a new site from SourceForge and > AppDynamics. Performance Central is your source for news, insights, > analysis and resources for efficient Application Performance Management. > Visit us today! > http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ Introducing Performance Central, a new site from SourceForge and AppDynamics. Performance Central is your source for news, insights, analysis and resources for efficient Application Performance Management. Visit us today! http://pubads.g.doubleclick.net/gampad/clk?id=48897511&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
