Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever?

From: Matias Machado <>
Date: Wed, 26 May 2021 17:14:38 -0300 (UYT)

Dear David,

Just a curiosity appealing to your vast knowledge of the AMBER code...

Aren't bonds defined according to the shortest distance criteria in PBC?

Otherwise, I can't imagine how AMBER deals with molecules (e.g proteins) that split through PBC images...

I mention that because this subject has pooped up before in the mailing list []... and I recall Tomas Bishop saying he was able to simulate bonds across periodic boundaries for DNA...

If that is the case, then creating bonds across PBC just requires correctly defining the box boundaries, no extra code is needed... am I right? :-/

All the best,


----- Mensaje original -----
De: "David A Case" <>
Para: "AMBER Mailing List" <>
Enviados: Miércoles, 26 de Mayo 2021 10:08:31
Asunto: Re: [AMBER] Covalent bonds across periodic boundaries supported yet/ever?

On Thu, May 20, 2021, Tucker Burgin wrote:

>GROMACS can support covalent bonds across a periodic boundary. I am
>interested in converting a GROMACS model that makes use of this feature for
>use with Amber using ParmEd's gromber command, but it appears that Amber
>doesn't know how to handle these bonds correctly.

You are correct: Amber doesn't allow for such bonds. I'm not aware of any
efforts to change this.


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Received on Wed May 26 2021 - 13:30:02 PDT
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