On 15/07/16 14:12, Albert wrote: > > > I found the following difference between Gaff 1.x and GAFF 2: > > 1. All the sp2 carbon in a AR2 ring (such as pyrrole, furan, pyrazole) > are either ’cc’ or ’cd’ atom types (not > ’c2’ any more). This is suggested by Gabriel Rocklin from UCSF. This > modification improves the planarity > of multiple-ring systems > > 2. New van der Waals parameters have been developed for ’br’ and ’i’ > atom types. The current parameters can > well reproduce the experimental density data of CH3 Br (1.6755, 20 > degree) and CH3 I (2.2789, 20 degree): > 1.642 for CH3 Br and 2.25 for CH3 I, in contrast, the old parameters > give 1.31 and 1.84, respectively.[325] > > 3. New van der Waals parameters have been suggested by David Mobley for > ’c1’, ’cg’ and ’ch’ atom types.[326] > > 4. We have performed B3LYP/6-31G* optimization for 15 thousands marketed > or experimental drugs/bio- > actives. Reliable bond length and bond angle equilibrium parameters were > obtained by statistics: each bond > length parameter must show up at least five times and has a rmsd smaller > than 0.02 Å; each bond angle > parameter must show up at least five times and has a rmsd smaller than > 2.5 degrees. Those new parameters > not showing up in old gaff were directly added into gaff 1.4; and some > low-quality gaff parameters which > show up less than five times or have large rmsd values (>0.02 Å for bond > length and >5 degrees for bond > angles) were replaced with those newly generated. In summary, 59 low > quality bond stretching parameters > were replaced and 56 new parameters were introduced; 437 low quality > bond bending parameters were > replaced and 618 new parameters were introduced. > > > I don't know whether people would like to implement this new GAFF2 into > BABEL............... > Yes, BUT! What Babel version are you using? We have recently implemented an updated gaff.prm in OB (if you download the git version you will find it). It was very difficult to get everything close to perfect. We compared the assignments due to Antechamber and OB, and tried to fix OB as good as we could. However Antechamber had errors as well (compared to the Wang2005 paper).
So there are TWO issues, first the force field parameters, and second the atom typing. Both should be treated in one go. > > On 07/14/2016 03:54 PM, David Hall wrote: >> Is there documentation beyond the Amber source code? Do you know if >> the difference is just using gaff2.dat instead of gaff.dat? > > > > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > 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 ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
