Re: [AMBER] query parameter files for mercuric ions

From: Pengfei Li <>
Date: Thu, 7 May 2015 09:52:21 -0400

Hi Ya,

There are several options you can choose in AMBER: the nonbonded model,
bonded model and cationic dummy atom model to simulate the metal ion.

Here is a tutorial about metal ion modeling:

Here are two papers about nonbonded model of divalent metal ions and the
parameters are all available in AMBER (please check *Amber force
fields-->Molecular mechanics force fields-->Ions *section in AMBER2015

If you have any questions, please feel free to email me.



2015-05-07 9:18 GMT-04:00 Ya Gao <>:

> Dear all,
> I need parameter files for mercuric ion (Hg2+), which is linked to GLU,
> CYS, and GLN, to perform simulations. However, I cannot find it in
> parm99.dat . Would anyone give me some help or tell me any source where
> these can be available.
> Thanks very much.
> Best wishes,
> Ya
> _______________________________________________
> AMBER mailing list

Pengfei Li
Ph.D. Candidate
Merz Research Group
Department of Chemistry
Michigan State University
AMBER mailing list
Received on Thu May 07 2015 - 07:00:04 PDT
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