Thanks Albert, by reference,I mean a Paper published in a Journal, with
citation, perhaps including and describing all the details you mentioned
here and more!
Alan
On 18 January 2017 at 06:53, Albert <mailmd2011.gmail.com> wrote:
> 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 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.
>
> regards
>
>
> On 01/17/2017 11:36 PM, Alan wrote:
> > Is there one?
> >
> > Thanks,
> >
> > Alan
>
>
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>
--
Alan Wilter SOUSA da SILVA, DSc
Senior Bioinformatician, UniProt
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom
Tel: +44 (0)1223 494588
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Received on Wed Jan 18 2017 - 00:30:03 PST
