Re: [AMBER] Strong Na+-ASP interactions

From: Carlos Simmerling <>
Date: Fri, 9 Feb 2018 10:00:43 -0500

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 - 07:30:03 PST
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