Re: [AMBER] Solvation of a long protein

From: Jason Swails <>
Date: Fri, 1 May 2015 11:48:03 -0400

On Fri, May 1, 2015 at 10:39 AM, Steven Ramsey <> wrote:

> Dear Amber Users,
> I am attempting to prep a protein in explicit solvent that is a 4 helix
> bundle, ~ 100 residues long on each helix. I want to minimize the size of
> my solvent box, but it turns out that the pdb of the structure has it
> diagonally oriented in space, thus the solvatebox command in leap sets it
> in a box where the protein runs along the diagonal.
> So I have a two part question: 1) Is there a good way to translate my
> protein structure so that it is not diagonal in space (without disrupting
> previous work/ introducing strain)?
> 2) Is there a better shape to use in general for minimizing solvent atom
> count, but especially in protein systems that are only large in one
> dimension?

‚ÄčThis depends. If your system freely rotates, using a rectangular prism
shape could be problematic if the axis of the protein rotates in such a way
that it will span multiple boxes (which would bring it into close contact
with its periodic images in the shorter dimensions of the unit cell). This
can introduce fairly severe artifacts.

You can always choose a more spherical shape for the unit cell -- like the
truncated octahedron -- which uses significantly fewer solvent to achieve
the same solvent buffer distance as a cube would. This would introduce a
bigger cell (and therefore more waters) than a rectangular box that "hugs"
the protein along its long axis, but it will also let the protein freely
tumble without crossing multiple unit cells.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Fri May 01 2015 - 09:00:02 PDT
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