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............... 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
