Re: [AMBER] zn parameters

From: Jacopo Sgrignani <>
Date: Thu, 6 Oct 2016 15:53:10 +0200

Dear Stefania
I had a look to the 1991 paper and as I remembered it is a bonded model
(i.e. you have covalent bond between ligands and the metal ion).
The 2014 paper seems to be a non-bonded model.
In my experience non-bonded models usually do not rigidly conserve the
coordination over the simulation.



2016-10-06 15:34 GMT+02:00 Stefania Mirabella <>:

> 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
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Received on Thu Oct 06 2016 - 07:00:03 PDT
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