Good suggestion. I actually did try that, but discovered it too has some problems with bond-order perception in simple polypeptides. Also discovered that Chimera can't display bond orders, but Jmol can.
For the time being, I've found a structure I can use that I assigned and fixed in the old InsightII program long ago. But eventually, I'll have to figure out a way. Thanks, Richard > On Jul 12, 2021, at 7:47 PM, Francois Berenger <mli...@ligand.eu> wrote: > > Dear Richard, > > Others might know more, but as a workaround you might try UCSF Chimera in > order > to do the PDB to MOL2 conversion. > > Regards, > F. > > On 09/07/2021 19:52, Richard Gillilan wrote: >> 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 _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
