AMBER Archive (2007)

Subject: Re: AMBER: Problem with modelling ammonium ion?

From: David Cerutti (dcerutti_at_mccammon.ucsd.edu)
Date: Wed Sep 05 2007 - 00:22:50 CDT

It appears my input files accidentally superimposed two atoms. I have a
handy little program that "mixes" different buffers for me using N copies
of whatever PDB files I give it. It does a fine job of not letting atoms
overlap by whatever distance you give it, but if the original PDB
describing the residue is messed up, no luck.

Things are working now.

I would be very grateful if someone knew of some ammonium sulfate
parameters, though. My course at the moment is to parameterize it based
on fitting a density profile for various concentrations of the salt, and
hopefully some additional data but who knows.

Dave
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