AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
Date: Tue Dec 18 2007 - 20:34:26 CST

Sorry for being imprecise..

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

Lars

On Dec 18, 2007 7:36 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
> > We are simulating a protein of ~7500 residues using PME with pmemd. It
> > is quite negatively charged, so we added ~250 counter ions (Na+) with
> > the Leap (function addIons). The protein is really unstable, which is
> > not what we expected.
>
> Did you add water too?
>
> Bill
>
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