On 09/01/17 17:57, Eiso AB wrote: > hmm, strange. > how do you look at the structure? Generate an sdf with babel instead of a mol2 and then visualize with avogadro (pdb with pymol works just as well).
We will look into the GAFF atom typing (my group did the last update). > creating a svg with obabel and -osvg actually seems to > repair the problem when the input is a mol2 file but not if it's a pdb file > > could you try this: > > obabel -ismi 454.smi -O 454.mol2 --gen3D -h > obminimize -ff GAFF -o pdb 454.mol2 > 454-gaff.pdb > > and > > rasmol 454-gaff.pdb > > The attached screenshot is what I get. > > > > On Mon, Jan 9, 2017 at 4:30 PM, David van der Spoel > <sp...@xray.bmc.uu.se> wrote: >> 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 -- 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 ------------------------------------------------------------------------------ Developer Access Program for Intel Xeon Phi Processors Access to Intel Xeon Phi processor-based developer platforms. With one year of Intel Parallel Studio XE. Training and support from Colfax. Order your platform today. http://sdm.link/xeonphi _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
