Hi!
I am Stefania and I would like to ask your help. I am using Amber 12
to perform a MD of a complex of a ligand with a metalloprotein,
containing Zn.
This Zn is coordinated to two Histidine residues (HID) in all the
reported X-ray crystallogrphic studies and in all the reported
dynamics with this protein, so I would like to mantain this kind of
coordination during my dynamics.
Initially, I tried with the zinc frcmod file with the older parameters
published by Merz in 1991 for TIP3P water solvatation (JACS 1991, 113,
8262)
Zn2+ 1.100 0.0125000
and in this case the coordination with histidines was kept, as it
seems more reasonable.
Then, I found out the newer Zn parameters reported by Merz in 2014
(JCTC 2014, 10, 289)
Zn2+ 1.455 0.02662782
In this case the coordination of the Zinc changes a lot during the
dynamics, loosing the coordination of one Histidine and also of my
ligand.
So, it seems less reasonable if compared with other dynamics performed
with similar ligand.
What do you think it could be the problem? What is the difference
between the two sets of VdW parameters?
P.s. the protonation of Histidines was the same for both the performed dynamics.
Thank you very much!
My best regards,
Stefania
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 06 2016 - 07:00:02 PDT
