[AMBER] Specifying size of truncated octahedron box manually

From: Bellesis, Andrew G <AGB53.pitt.edu>
Date: Tue, 6 Aug 2019 14:29:57 +0000

Hi all,

I am trying to set the dimensions of a truncated octahedron box in tleap manually.

Here is the context of my problem: I am simulating folding and unfolding of proteins. When I start with the folded state, I want to make sure that my solvent box is big enough to accomodate the resulting unfolded state + 12 Angstrom clearance. Therefore, to try and find the right box size to start with, I solvated a known unfolded structure to obtain the following box information:

> solvateOct x SPCBOX 12.0
Scaling up box by a factor of 1.177857 to meet diagonal cut criterion
  Solute vdw bounding box: 79.955 83.697 84.429
  Total bounding box for atom centers: 112.697 112.697 112.697
      (box expansion for 'iso' is 4.8%)
  Solvent unit box: 18.774 18.774 18.774
The number of boxes: x= 7 y= 7 z= 7
  Volume: 734885.482 A^3 (oct)

I want to take the box defined here and the use it when I solvate the smaller folded protein. How do I do this?

Andrew Bellesis
University of Pittsburgh
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Received on Tue Aug 06 2019 - 08:00:02 PDT
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