Re: [AMBER] How best to build a solvent box for a solute with changing dimensions?

From: Daniel Roe <>
Date: Mon, 7 Aug 2017 12:26:13 -0400


On Mon, Aug 7, 2017 at 11:53 AM, Kasprzak, Wojciech (NIH/NCI) [C]
<> wrote:
> 1) How best to build a solvent box big enough to accommodate the expected range of motions of the solute?
> Could I overlay the extreme states observed in implicit solvent runs, create a solvent box around them,
> then remove all but the initial state and "refill the voids" with solvent? What LEaP commands would
> accomplish this, or what is the correct protocol to follow? I'd like to avoid expanding the box size via
> larger and larger "distance" parameter in the solvateBox command.

Not sure what the best option here is. Unfortunately I don't think
leap can do exactly what you describe. I think using extreme states is
a great way to start. What I would do is to solvate one of these
extreme states (or maybe generate what amounts to a fully extended
state) with an adequate buffer and count how much solvent is added.
Then I would use that number as a target with something like this
script: It's not super efficient
but it will get the job done. Something like packmol may be better
suited to this but I don't have a lot of experience with that program.

> 2) How would I test if the large scale PBC breach (by a part of the solute) leads to interactions/interference
> between periodic solute images?

You can try using the 'minimage' command in cpptraj, which will report
the minimum non-self imaged distance between atoms.


> Any comments or pointers to tutorials would be much appreciated.
> Thank you in advance, Voytek Kasprzak
> Wojciech (Voytek) Kasprzak (Contractor)
> Analyst Programmer
> Frederick National Laboratory for Cancer Research
> Leidos Biomedical Research, Inc.
> Post Office Box B
> Frederick, Maryland 21702
> Phone: 301-846-5537
> _______________________________________________
> AMBER mailing list

Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Mon Aug 07 2017 - 09:30:03 PDT
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