AMBER Archive (2006)

Subject: Re: AMBER: saltcon with explicit water?

From: Kenley Barrett (kenley.barrett_at_gmail.com)
Date: Wed Apr 12 2006 - 18:07:44 CDT

Thank you very much for your reply. I have a couple of questions about using
"addIons" that I didn't understand when using the manual.

Is it okay to use the addIons command twice, once to neutralize the system
and a second time to add a given concentration of salt?

I don't totally understand the syntax "addIons unit ion1 numIon1 [ion2
numIon2]". Is "numIon" literally the number of ions of that type, or can I
enter it in terms of concentration? My goal is to add 0.1 M KCl.

Please let me know your thoughts. Thank you very much for your help, I
really appreciate it.

Kenley

On 4/12/06, David A. Case <case_at_scripps.edu> wrote:
>
> On Wed, Apr 12, 2006, Kenley Barrett wrote:
> >
> > Does the SALTCON command work with
> > explicit solvent?
>
> No; it only has an effect with implicit solvent.
>
> > If not, is there another way that I can add salt?
>
> Use the "addIons" command in LEaP to generate explicit ions (to go along
> with
> your explicit water molecules!)
>
> ...good luck..dac
>
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