Re: [AMBER] Calcium forcefields

From: Zuo, Zhicheng <>
Date: Wed, 18 Jul 2018 14:30:39 +0000


You may refer to the recent paper from our lab:


Identification of a unique Ca<sup>2+</sup>-binding site in rat acid-sensing ion channel 3<>
Acid-sensing ion channels (ASICs) sense changes in extracellular acidity with Ca2+ as an allosteric modulator and channel blocker. Here authors use electrophysiology and molecular dynamics simulation to identify the residue in ASIC3 which modulates proton sensitivity and contributes to the Ca2+ block.

In this work, we employed two different Ca2+ models, i.e. point charge (soft-sphere) and multisite (a.k.a dummy atom) models, for

simulations of Ca2+ binding membrane proteins. And you will see that very similar results were derived with the two models.

Specifically we recently finished a benchmark work (just submitted) wherein we assessed the performance of all four types of non-bonded Mg2+ models (i.e. the point-charge models based on a 12-6 or 12-6-4 potential, and the multisite models based on a 12-6 or 12-6-4 potential)

in terms of reproducing a challenging crystallographic configuration in a nuclease system. It turns out that the 12-6-4 multisite model performed the best in maintaining the crystallographic coordination patterns and also exhibited good capability in attaining a correct carboxylate denticity.

It depends on the system and the scientific question to be answered. For your case, I think either the bonded or non-bonded models is appropriate,

considering that Ca2+ plays a structural role only. In the enzyme systems, special attention should be given.

Zhicheng Zuo

From: Aashish Bhatt <>
Sent: Tuesday, July 17, 2018 10:35:59 PM
To: AMBER Mailing List
Subject: Re: [AMBER] Calcium forcefields

Daer Piotr

In amber only for Ca2+, force field is available. check *source
leaprc.water.opc* and for Ca2+ keyword is* CA*.

Aashish Bhatt

On Tue, Jul 17, 2018 at 11:06 PM, Piotr Fajer <> wrote:

> Forcefields for Ca2+ :
> I am attempting to simulate behavior of calcium binding EF-hand proteins.
> Is there a developed forcefield, parameters for Ca2+ ion similar to ZAAF
> for zinc ion developed by Li&Merz ?
> Thanks
> Peter
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