(forwarding to the list) On 25 August 2013 06:05, Morency, Louis-Philippe <louis-philippe.more...@usherbrooke.ca> wrote: > Excellent question you asked. I'm trying to convince my colleagues to drop > the pdb format in favor of the mol2 format but, actually, we use the pdb > format as output in a molecular docking software we develop because it's > common (even if you lose a lot of precious informations compared to other > formats). Until we update the software, I'm still looking for an easy way to > add explicit hydrogens to a docking pose and I would like to know something > in OpenBabel API could help into adding hydrogens from the original ligand > structure (mol2 format) and a ligand conformation (without hydrogen) in pdb > format. > > Thanks for your answer, > > Louis-Philippe Morency > > On 2013-08-24, at 17:53, "Noel O'Boyle" <baoille...@gmail.com> wrote: > >> 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
