AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: David A. Case (case_at_scripps.edu)
Date: Wed Dec 19 2007 - 14:01:55 CST

On Wed, Dec 19, 2007, Pablo Englebienne wrote:

> >Yes, water was added after adding the ions as recommended in the amber
> >manual. The number of counter ions added corresponds to the charge of
> >the protein so it is neutralized, ofcourse. :-)
> >
> >charge mol
> >addIons mol Na+ 250
> >solvateBox mol TIP3PBOX 8

Of course I don't know why a 7500 residue system is "really unstable", but you
should look (visually) at the distributions of ions you get. Also, it is
certainly worth solvating *before* the addIons step: that is what I would
recommend, and I don't know where in the manual it states otherwise(?).

...dac

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