Dear list, we're struggling with getting OB to produce the right gaff atom parameters.
We start from a Gaussian log file (http://folding.bmc.uu.se/1-ethyl-3-methylimidazolium3-esp.log.gz). Then, using obabel -ig09 1-ethyl-3-methylimidazolium3-esp.log.gz -omol2 koko.mol2 we find the ring atom types are not aromatic. Alternatively using obenergy -ff GAFF 1-ethyl-3-methylimidazolium3-esp.log.gz we can see that the incorrect atom types for the ring atoms are produced. Incidentally, we have fixed some minor things in gaff.prm, but dealing with aromatics is harder. Meddling with gaff.prm does not solve it. In addition, the gaussformat.cpp file explicitly sets the total charge of the molecule (all the way at the end, I may have added this previously), but this is apparently not used in kekulizing. mol.SetTotalCharge(charge); Any clue would be appreciated, but it seems there are errors in smarts parsing code as well as in gaff.prm A correct sdf generated by open eye software can be found at the pubchem site here: http://pubchem.ncbi.nlm.nih.gov/vw3d/vw3d.cgi?cmd=crtvw&reqid=1553910336500617460# Cheers, -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell & Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.se http://folding.bmc.uu.se ------------------------------------------------------------------------------ Subversion Kills Productivity. Get off Subversion & Make the Move to Perforce. With Perforce, you get hassle-free workflows. Merge that actually works. Faster operations. Version large binaries. Built-in WAN optimization and the freedom to use Git, Perforce or both. Make the move to Perforce. http://pubads.g.doubleclick.net/gampad/clk?id=122218951&iu=/4140/ostg.clktrk _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
