AMBER Archive (2008)

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

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Sep 29 2008 - 15:13:05 CDT

Hi:
Please see infra.

On Mon, Sep 29, 2008 at 8:38 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>> As the
>> conformation of the molecule is expected to depend from the vdw
>> assigned to Cl-, and that vdw is certainly not a constant for
>> different environments (Linus Pauling's story), in which file could
>> the vdw be changed? Certainly I should check now again the distances
>> from chloride and its ligands.

I did nothing more to this regard as I am busy organizing to determine pKa.

>
> The Cl- vdw parameters have been developed for a water bath. The
> TIP3 water uses a single vdw on the O, large enough to encompass the
> H's too. Thus the parameters derived for the ion in water may not give
> distances to solute atoms that agree with experiment. This was shown
> for cations in
>
> 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).

That is interesting and useful.

>
> 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?

Thanks
francesco

>
> Bill Ross
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