Thanks for the info Dave - I’ll be looking out for more material on the subject.
I’m new to charge derivation portion of MD, so apologies if this is obvious - How does the use of MD-derived solution phase charges improve the ‘real life’ behaviour of the ligands? And would such a protocol also be applicable to the protein (receptor)?
My ligands are in the range of 18-24 C-atom long, in various single/double bond and/or ring configurations with a carboxylic acid head. Akin to poly-unsaturated fatty acids with some modifications.
Cheers,
Kavin
On 23 Feb 2016, at 16:04, David Cerutti <dscerutti.gmail.com<mailto:dscerutti.gmail.com>> wrote:
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<mailto: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<mailto: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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Received on Fri Feb 26 2016 - 03:00:10 PST
