Re: AMBER: PME and counter ions

From: Bill Ross <>
Date: Wed, 19 Dec 2007 12:14:19 -0800 (PST)

> 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(?).

Doing addIons this way reduces gaps in the solvent.

Also, how did you equilibrate? (Not sure if this was mentioned before.)

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Received on Sun Dec 23 2007 - 06:07:09 PST
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