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

From: David A Case <>
Date: Sat, 13 Nov 2021 08:37:05 -0500

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.


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Received on Sat Nov 13 2021 - 06:00:02 PST
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