How big are your ligands, Kavin?
There is also a functionality in Amber mdgx for deriving charges. It uses
a REsP-like protocol, but as I'll be discussing at some length at the ACS
it derives two sets of charges: one appropriate to the vacuum phase, the
other appropriate to the condensed (aqueous) phase. What you then do is
complete your force field parameters with vacuum-phase quantum data and the
vacuum phase charges, then take those parameters and combine them with the
solution-phase charges to do your actual simulation. The mdgx protocol
streamlines the process of getting the solution-phase appropriate charge
set, which involves inserting the solvent charge density from an MD
simulation into what is otherwise a REsP procedure to obtain the polarized
wave function. I don't have a tutorial for it yet, but I am working with
an undergraduate to do this for about 600 compounds, so any additional
experience would then help me to design a tutorial for the Amber website.
If you want fast answers, RED / Amber GAFF is probably the way to go, but
bear in mind that a charge set that comes "pre-polarized" makes it
(philosophically) tricky to design the rest of the force field.
Dave
On Tue, Feb 23, 2016 at 10:48 AM, Abelak, Kavin <kabelak.rvc.ac.uk> wrote:
> You’re quire right about R.E.D. Server - I was being blind and led astray
> by the numerous “Cannot run Java applet” security prompts and thus had
> failed to use it previously.
>
> Thanks,
> Kavin
>
>
>
> > On 19 Feb 2016, at 17:24, David A Case <david.case.rutgers.edu> wrote:
> >
> > On Fri, Feb 19, 2016, Abelak, Kavin wrote:
> >>
> >> I find myself needing to derive charges for some non-standard
> >> ligands. I’ve had a brief search through the archives
> >> and tutorials, and keep getting referred to tutorial A1
> >> (http://ambermd.org/tutorials/advanced/tutorial1/section1.htm). Is this
> >> still the currently accepted method for running charge derivations using
> >> Gaussian? I only ask as it is dated 2008 and cites Amber 10 (and older).
> >
> > The standard charge derivation procedure has not changed since forever
> (i.e.
> > since the early 1990's). So the tutorial should still be OK, but be
> sure to
> > read the caveat there (in bold type).
> >
> >>
> >> Another related question is: are there other streamlined methods
> >> (similar to R.E.D Tools) that anyone can suggest?
> >
> > Why not use R.E.D. Tools itself? That is the most popular way, as far
> as I
> > can tell. They maintain a large-ish database that may already have your
> > ligand, or something close to it.
> >
> > ....dac
> >
> >
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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Received on Tue Feb 23 2016 - 08:30:04 PST
