AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Tue Sep 30 2008 - 05:05:13 CDT

Hi:
While I have now your paper for study, may I ask if X-ray diffraction
data for the complexed chloride ion could help. I have such data at 2A
 resolution quality.
Thanks
francesco

On Tue, Sep 30, 2008 at 12:03 AM, Bill Ross <ross_at_cgl.ucsf.edu> 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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