AMBER Archive (2008)

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

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Sep 29 2008 - 13:38:46 CDT

> 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.

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).

I believe the first peak of the radial distribution in dynamics would be
the ideal measurement to consider.

Bill Ross
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