AMBER Archive (2006)

Subject: Re: AMBER: Simulating proteins with calcium ion

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Tue Dec 12 2006 - 13:47:48 CST

> You will want to come up with some way to verify that
> whichever force field you use is giving reasonable
> results.

Comparing the radial distribution function with experiment is a
standard option. This works for ions in water, but for ions in
complex with other molecules the water-derived ion parameters may
not be ideal since waters are usually parameterized for water-water
interactions, e.g. TIP and SPC have oversized O to enclose the
vdw-less H's. These considerations may be secondary to the effect
of large charges in a point-charge model.

Bill
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