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 Custom Video Creation Service <https://jobs.vidzzy.com/hire-custom-video-creation-service/> 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
