Hello all, I'm actually back to this list after nearly twenty years. Nice to see this package is still actively maintained!
It will take me a while to get back up to speed, but my needs are the same as they were back then when I published some docking work using the code: I use openbabel to convert pdb files to mol2 adding bond orders and protonation states for proteins. My code then uses the bond orders to assign forcefield parameters for simulation purposes. I did a preliminary conversion of lysozyme: obabel -p 7.0 -ipdb 6lyz_no_wat.pdb -omol2 >! test.mol2 Seems like there are a number of incorrect bonds formed. I have a very old note that openbabel often failed to assign carbonyl oxygens a double bond. In principle, knowledge of the amino acid 3-letter code should solve the bonding problems. Anyone worked on this aspect of openbabel in the past? Richard Gillilan HP-Bio/BioSAXS Cornell High Energy Synchrotron Source Ithaca, NY _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
