How are you visulizing the box, i mean what software ?
Arun
On Mon, 12 Jan 2026, 07:02 Sree Gouri Menon via AMBER, <amber.ambermd.org>
wrote:
> Dear AMBER users,
>
> I am encountering an issue with solvation box generation in tleap and would
> appreciate some guidance.
>
> I am studying aggregation and have placed 10 copies of my molecule in a box
> to create the initial configuration. After loading this system into tleap
> and adding water and ions, the solvation box generated by tleap does not
> fully enclose all 10 molecules. In particular, 1–2 molecules extend outside
> the box boundaries, and the box itself appears poorly positioned relative
> to the solute.
>
> I have tried increasing the solvation box size (using larger buffer
> distances / box dimensions), but the problem persists — the box still does
> not accommodate all molecules. This is confusing because the original
> structures were generated inside a cubic box of ~15 nm per side, and the
> solvation box dimensions I specify in tleap are larger than this. I have
> attached an image showing the issue for clarity.
>
> Is there a recommended workflow to ensure that all molecules are properly
> enclosed before solvation (e.g., recentering, resetting the unit cell, or
> specific tleap commands)?
>
> Any suggestions or pointers would be greatly appreciated.
>
> Thank you for your time and help.
>
> Best regards,
> Sree Gouri
> [image: image.png]
>
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Received on Sun Jan 11 2026 - 23:30:05 PST
