AMBER Archive (2008)

Subject: Re: AMBER: Leap atoms CL and OXT do not have a type

From: Francesco Pietra (
Date: Thu Oct 02 2008 - 10:47:31 CDT

I am planning to get the radial distribution vs the distance between
chloride ion and protein-atom which I know experimentally to be
closest. This for all protein atoms in this situation. Using the vdw
provided by Amber for chloride ion.

A point of my concern is that the protein atoms at issue are on amino
acid side chains, in a couple of cases they belong to carboxylates
that, as they come from leap, are not protonated. From the X-ray
electron density map it is not entirely clear if, in such a case, it
was CO2- or CO2H, and thus the interaction with Cl- is even less
clear. Whether CO2- or CO2H depends on the pH the protein has sensed.

I am also organizing to measure pKa of the amino acids with software
that, via monte carlo, explores the various conformational situations.

Thus, at which stage should the radial distribution procedure be best
carried out?

Unless this question would require the Aladino's lamp.


On Tue, Sep 30, 2008 at 12:03 AM, Bill Ross <> wrote:
>> > I believe the first peak of the radial distribution in dynamics would be
>> > the ideal measurement to consider.
>> Could you please address me where to learn about, and, should you find
>> the time, vulgarize a bit this last sentence?
> You could read the paper I referenced:
> Ion-Induced Stabilization of the G-DNA Quadruplex:
> Free Energy Perturbation Studies. W.S. Ross and C.C. Hardin
> Journal of the American Chemical Society 116, 6070 (1994).
> Radial distribution is represented by a graph of the density of one type
> of atoms around another, where the x-axis is distance, averaged over all
> cases of interest in a trajectory. The first peak represents the average
> distance of the closest pair(s). Ptraj can calculate radial distribution.
> Bill
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