Thank you very much, David. I will try the suggestions.
-----Original Message-----
From: David A Case [mailto:david.case.rutgers.edu]
Sent: Monday, February 12, 2018 7:51 AM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Strong Na+-ASP interactions
On Fri, Feb 09, 2018, Rui, Huan wrote:
>
> 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.
First thing to try is to upgrade to the current version of AmberTools (not sure what you are using now), and switch to ff15ipq, which upgraded the way salt bridges and ionic interactions are represented. (See the references in the Amber 2017 Reference Manual for more info.)
ff15ipq was develped with spc/e water in mind, so that is probably the first thing to try. We now match ion parameters with water models, automatically, when you source a leaprc.water.xxxx file: see the Reference Manual for more info.
...good luck....dac
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Received on Mon Feb 12 2018 - 07:00:02 PST
