Re: [AMBER] Coordinate of excess charge (proton)

From: Adrian Roitberg <>
Date: Mon, 23 Sep 2013 17:51:41 -0400

Hi Fabricio. Just out of curiosity, can you point to a recent paper on
this ?
I believe I know what they mean, but it is not a coordinate used a
restraint, but rather a coordinate to analyze on. Basically, run the
sampling in whatever coordinates you deem proper, and project onto a
charge coordinate.

I cannot imagine how to control the location of the charge in qm or
qm/mm, unless you go all out to constrained DFT or some very advanced


On 9/23/13 5:48 PM, Fabrício Bracht wrote:
> Hi there. This is more of a personal doubt than an actual problem. Since I
> started working with qm/mm I have noticed that lots of papers cite the
> "coordinate of excess charge" method to study proton transfers, especially
> the ones that follow the Grotthuss mechanism. Since proton transfer is a
> process that enzymes are quite fond of, I was wondering if there is any
> plan on implementing this type of restraint in amber.
> Thank you
> Fabrício
> _______________________________________________
> AMBER mailing list

                             Dr. Adrian E. Roitberg
Colonel Allan R. and Margaret G. Crow Term Professor.
Quantum Theory Project, Department of Chemistry
University of Florida
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Received on Mon Sep 23 2013 - 15:00:04 PDT
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