I'll take a look at the sources and see if I can figure out when they'll
fail, and use GAFF->MMFF94->UFF.
Thanks for the feedback!
Dave
On Mon, Feb 4, 2013 at 1:22 PM, Geoffrey Hutchison <
geoff.hutchi...@gmail.com> wrote:
> > Speed? Should make no difference at all. Lennard Jones + Coulomb on
> > point charges. It is rather not for proteins (that is regular Amber) but
> > for small (organic) ligand molecules.
>
> I stand corrected. I should point out that David really does this for a
> living. In comparison, I just pretend. :-)
>
> So David, I guess I'd go with GAFF first, MMFF94 fall-back, UFF second
> fall-back. By its nature, UFF should work for essentially any chemistry.
>
> As for speed, both Tim and I spent time going through the Open Babel
> implementations of MMFF94 and UFF to minimize sqrt(), etc. IIRC, this was
> good for 10-20% improvement. I don't think anyone has really looked at the
> GAFF implementation.
>
> Thanks for the suggestions David!
> -Geoff
>
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