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.
Best,
Huan
Huan Rui, Ph.D.
Scientist
Amgen Inc.
360 Binney Street
Cambridge, MA 02141
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Received on Fri Feb 09 2018 - 07:00:03 PST
