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 - 05:00:03 PST
