Re: [AMBER] Reference for GAFF2?

From: Albert <mailmd2011.gmail.com>
Date: Wed, 18 Jan 2017 07:53:44 +0100

There are plenty of new things have been optimized in the GAFF2
according the reference file of AMBER 16:


We have modified some parameters according to users feedback. We would
like to thank users who provide
us nice feedback/suggestion, especially David Mobley and Gabriel
Rocklin. This version (GAFF1.4) is a meta-
version between gaff1.0 and gaff2.0 and the following is the major changes:

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 ; 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 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.

regards


On 01/17/2017 11:36 PM, Alan wrote:
> Is there one?
>
> Thanks,
>
> Alan


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Received on Tue Jan 17 2017 - 23:00:04 PST
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