Re: [AMBER] Adding ions at a particular position

From: Gustaf Olsson <>
Date: Wed, 9 Sep 2020 07:08:27 +0000

There should be many different solutions to this problem

- I think it should be possible to change the position of an ion/atom using the edit mode in xleap.
- You could assemble the system using packmol where you can control the location of the molecules you are adding.
- You could use a GUI program (like Avogadro/pymol or similar) to place the ion in a reasonable position.
- You could likely “guide” the ion into the correct position through simulation with distance restraints/steering.

Best regards
// Gustaf

> On 9 Sep 2020, at 06:14, Athena N <> wrote:
> Dear all,
> I wanted to know how to add ions at a particular position of a biomolecule
> in AMBER. My objective is not to neutralize the system, instead the ions
> are required for the catalytic activity of a protein or in other cases like
> G-quadruplexes in the core of the system. How to place these ions into the
> system? I have related protein models which has the ions and can be used to
> add tjese ions. In such cases how to proceed? And if I do not have a model,
> what is the procedure?
> Thanking you in advance
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Received on Wed Sep 09 2020 - 00:30:02 PDT
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