Re: [AMBER] Strong Na+-ASP interactions

From: Rui, Huan <>
Date: Fri, 9 Feb 2018 16:39:06 +0000

Thanks, Carlos, for pointing this out. I think I can just use ff14SB for now. Hopefully this is the problem.


-----Original Message-----
From: Carlos Simmerling []
Sent: Friday, February 09, 2018 10:01 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Strong Na+-ASP interactions

Others like Dave Cerruti may be able to give more insight, but at first glance I would suggest that since the ipq force field was developed using TIP4P variant water, and using TIP3P might not work as expected.

On Feb 9, 2018 9:58 AM, "Rui, Huan" <> wrote:

Hi fellow AMBER users,

I newly switched from using running simulations with CHARMM force field to running simulations using AMBER force field. I have a questions about the ion carboxyl group interactions in the AMBER FF. I was running this simulations with these parameters:

source leaprc.ff14ipq
source leaprc.gaff
loadamberparams frcmod.ionsjc_tip3p
loadamberparams frcmod.ionslrcm_cm_tip3p

And I have NaCl and a Mg2+ ion in my system with TIP3P water. When I was looking at the trajectory, it seems like some Na+ ions would cling to the Asp in the protein for an entire 200 ns course. The ion concentration of the system is very low. I just added 7 Na+ to neutralize the system roughly of 40K atoms. I know that in CHARMM FF, we use NBFIX to alleviate the problem. I wonder if other users have seen things like this before in AMBER, and what is your ways of dealing with it. Another question would be what are the best ion parameters to use for the regular protein in the waterbox simulations?

PS: I also ran a test simulation with K+, but the strong ion-Asp pairs were not observed.

Thank you very much in advance.


Huan Rui, Ph.D.
Amgen Inc.
360 Binney Street
Cambridge, MA 02141
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Received on Fri Feb 09 2018 - 09:00:04 PST
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