Re: [AMBER] problem in locating Aqvist Mg2+ parameter in amber

From: David Case <>
Date: Tue, 23 Apr 2019 12:23:49 +0000

On Tue, Apr 23, 2019, ATUL KUMAR wrote:

>I am trying to set up a system with Mg2+ ions in it and I
>want to use the Aqvist parameters (J.Phys.Chem.1990,94,8021-8024) for the
>same. Where can I find these parameters in amber?

If you look at AMBERHOME/dat/leap/parm/parm99.dat, you will find
"adapted" Aqvist ion parameters. The original paper used different
mixing rules than Amber uses, so the "adaptation" sets the interaction
parameters for TIP3P water to be what was originally proposed. These
parameters would not make sense for other water models.

I feel constrained to point out that these parameters are nearly 30
years old, and that a lot of work (especially in the past few years) has
gone into exploring Mg2+ parameters designed to be used with many
different water models, and in a variety of circumstances. See the
references in the "Ions" section of the Amber 2018 Reference Manual.


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Received on Tue Apr 23 2019 - 05:30:03 PDT
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