Re: [AMBER] What ion parameters can be used with non-water solvents?

From: Pengfei Li <>
Date: Wed, 17 Nov 2021 18:59:01 -0600

Hi Matthew,

I would expect the ion parameters for water have reasonable transferability to other solvents, especially the solvents which are similar to water (e.g. methanol).


> On Nov 13, 2021, at 7:37 AM, David A Case <> wrote:
> On Sat, Nov 13, 2021, Matthew Guberman-Pfeffer wrote:
>> I want to test the stability (measured by RMSD) of a protein in
>> MeOH or CHCl3 versus water, but I’m wondering if I would still load
>> frcmod.ionsjc_tip3p to describe the neutralizing ions. Are there specific
>> ion parameters for these non-water solvents? I’d greatly appreciate any
>> suggestions (or warnings about proceeding).
> I don't know of any parameters for ion interactions with methanol or
> cholorform. Are you sure that you still have a charged protein (esp. with
> ChCl3)? If this is more of a model (or theoretical) study, you might
> consider not including ions, and let the uniform background charge from PME
> handle the neutralization.
> ....dac
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