Re: [AMBER] How to add metal ions?

From: Jason Swails <>
Date: Wed, 17 Jul 2013 09:49:17 -0400

On Wed, Jul 17, 2013 at 7:43 AM, 赵媛 <> wrote:

> Dear Amber users.
> We want to do some computations about the interaction between the metal
> ion and a small molecular. MD simulation is the first step. But we don’t
> know how to generate initial files just like “prmtop “and “inpcrd” files
> including metal ion and the molecular. How to add the metal ion into the
> small molecular? Could anyone help us or give me some examples about this?

See the following tutorial for building a residue that can be recognized by

Then you can add metal ions using the addIons command in leap (or
addIonsRand). The first tutorial ( shows an example
of using the addIons command to neutralize a system (although more details
can be found in the AmberTools manual).

I suggest that you work through a couple tutorials to get familiar with
using the Amber programs.

Good luck,

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
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Received on Wed Jul 17 2013 - 07:00:02 PDT
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