Re: AMBER: Simulating proteins with calcium ion

From: Bill Ross <>
Date: Tue, 12 Dec 2006 11:47:48 -0800 (PST)

> 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.

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Wed Dec 13 2006 - 05:22:05 PST
Custom Search