On 09/01/17 16:08, Eiso AB wrote: > (installation: Open Babel 2.4.0) > > I'm getting a distorted ring (the 5-ring) when using > obminimize with -ff GAFF > > 454.smi > OC1=CC=C(C=C1)C2=NN=C(O2)SCC#C > > obabel -ismi 454.smi -O 454.mol2 --gen3D -h > obminimize -ff GAFF -o mol2 454.mol2 > 454-gaff.mol2 > > when -ff GAFF is omitted the results look ok. > > Is this a bug or an omission in GAFF? > Anyway to detect of avoid these kind of issues with GAFF? Did you check whether the 3D structure looks OK? OK I verified it and it is fine. An N-N bond in a ring is problematic for atom type detection though. Indeed, detecting these problems should be trivial:
COULD NOT FIND PARAMETERS FOR BOND cp-nd, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR BOND cp-os, USING DEFAULT PARAMETERS SETTING UP ANGLE CALCULATIONS... COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-nd, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE ca-cp-os, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE nd-cp-os, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE cp-nd-nd, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE nd-nd-cd, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE nd-cd-os, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE cp-os-cd, USING DEFAULT PARAMETERS COULD NOT FIND PARAMETERS FOR ANGLE ss-c3-c1, USING DEFAULT PARAMETERS > > > best wishes, > > Eiso > > ------------------------------------------------------------------------------ > 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 > -- 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 ------------------------------------------------------------------------------ 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
