On 2014-03-05 22:30, David van der Spoel wrote: > 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, > Any pointers to where to start fixing this?
I'm happy to do some programming, but it seems the problems lie deeper in the code than in forcefieldgaff.cpp. -- 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
