Date: Mon, 12 Jan 2026 10:59:34 +0400
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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