Re: [AMBER] Adding Ions.

From: Dean Cuebas <deancuebas.missouristate.edu>
Date: Wed, 30 Jun 2010 23:29:39 -0500

Add the water first, then add the cations and anions separately.

Hope this helps

Dean
"If we begin with certainty, we shall end with doubt; but if we are content
to begin with doubt, then we shall end in certainty."
Stanislavski

Dr. Dean Cuebas dac012f.missouristate.edu,
Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897


> From: Ajay Ummat <ajayummat.gmail.com>
> Reply-To: AMBER Mailing List <amber.ambermd.org>
> Date: Wed, 30 Jun 2010 13:05:25 -0500
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: [AMBER] Adding Ions.
>
> I want to add 150mM Na+ Cl- ions in my system. I used the command: addions x
> Na+ 91 Cl- 96 (as my system had +ve 5 charge and I needed 96 each of Na+ and
> Cl-). When I visualize the result of adding ions, leap has added all the
> ions only on one particular side of the protein. This certainly seems
> unreasonable. Can anyone suggest me a way of uniformly distributing the ions
> around the protein. When I say uniformly I mean to consider eletrostatics of
> the distribution. A skewed distribution of charges would make my production
> run unrealistic and unreliable. Thanks in advance.
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Received on Wed Jun 30 2010 - 22:00:03 PDT
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