We're not responsible for Autodock - you might want to contact them. As far as small molecules getting large total charges, that's a bug - can you give us an example and file it at: https://github.com/openbabel/openbabel/issues
Thanks and best regards, -Geoff > On Jun 14, 2018, at 8:44 AM, MichaelSmith <michaelsmith8...@gmail.com> wrote: > > Hi, > > According to the 2006 J Comput Chem paper describing Autodock 4, OpenBabel > was used to add hydrogens and assign Gasteiger charges to the protein and > ligands that were used as the training set to calibrate the force field. I > just want to ask whether the -p option in OB was used to do this (where it > allows the user to specify a pH so that it can attempt to calculate > protonation states). There has been a bug discovered in this usage of > OpenBabel where very large charges can get assigned to molecules. I have > seen one example of a small molecule being assigned a total charge of -9, > when it reality it contains a single ionizable group.Can someone please > comment on whether this might have had an impact on the accuracy of > Autodock's force field? > > > Please help. > > I didn't find the right solution from the Internet. > > References:- > http://mgl.scripps.edu/forum/viewtopic.php?f=9&t=1398 > > Thanks! > > > > > > -- > Sent from: http://forums.openbabel.org/General-discussion-f3090658.html > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
