Re: [AMBER] Adding ions at a particular position

From: Dr. Anselm Horn <>
Date: Wed, 9 Sep 2020 09:57:05 +0200

To add a further possible solution to Gustav's list:
- You could use an (in this region) structural similar protein with an
ion present, do a structural superposition of the respective region with
your ion-free system, and then use the ion position in your protein of

Best regards,


> 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 - 01:00:02 PDT
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