Re: [AMBER] Chloroform box

From: David A Case <>
Date: Tue, 7 Oct 2014 07:30:20 -0400

On Tue, Oct 07, 2014, Neha Gandhi wrote:
> I am interested in simulating a protein in a nonaqueous solvent box
> (specifically, chloroform). I am aware that AMBER provides a
> pre-equilibrated chloroform box, but am interested in knowing how AMBER
> treats counterions in the presence of such non-aqueous solvents.

I'm not aware of any testing of Amber ion parameters with chloroform. So you
might want to some simple liquid simulations (no protein) first to see what

> Do I need to add counterions to my box in the presence of protein and
> chloroform?

No, this is not required.


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Received on Tue Oct 07 2014 - 05:00:02 PDT
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