Re: [AMBER] Chloroform box

From: Jason Swails <>
Date: Tue, 07 Oct 2014 07:52:18 -0400

On Tue, 2014-10-07 at 15:49 +0800, Neha Gandhi wrote:
> Dear List,
> 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.

Amber treats them exactly the same way -- they have exactly the same
parameters as they do when put in water. However, I don't think that
ionic salts are even soluble in chloroform (I don't know for sure, but
chloroform is not nearly as polar as water). If the salt is not soluble
in chloroform, it would not be appropriate to use them as counterions.
And the ion parameters were certainly not designed for use with

> Do I need to add counterions to my box in the presence of protein and
> chloroform?
> Your insight is greatly appreciated!

You can't assume that the ionization states that you'd find in the
aqueous phase is the same as what you would find in chloroform (do
proteins even exist in their zwitterionic states in chloroform?)
Charged protein residues ionize _because_ of water, and I doubt
chloroform would have the same effect on those residues.

I don't know enough about dissolving proteins in chloroform to suggest
what should be done, but I do not think simply using CHCL3BOX instead of
TIP3PBOX in tleap will do the trick. I also doubt the native fold of a
protein in water even resembles the "native" fold in chloroform.

You will probably have to do some more investigation in order to design
a reasonable model for a chloroform-dissolved protein.

Hope this helps,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Tue Oct 07 2014 - 05:00:03 PDT
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