How to control box size

From: pu xuemei <>
Date: Wed 22 Jan 2003 12:58:53 +0000

Dear Amber user
I solvate one enzyme with acetonitrile in xleap,as follows

 solvatebox x ACN 10.0
  Solute vdw bounding box: 56.888 45.091 46.347
  Total bounding box for atom centers: 76.888 65.091 66.347
  Solvent unit box: 6.343 4.237 4.237
  Total vdw box size: 69.769 67.795 67.795 angstroms.
  Volume: 320669.682 A^3
  Total mass 119968.943 amu, Density 0.621 g/cc
  Added 2309 residues.

The question is that I don't understand why x dimension(69.769) in "Total
vdw box size" is smaller than that (76.888) in "Total bounding box for atom
centers". Amber explain that "total vdw box size" is tatal bounding box for
solute+solvent atom centers plus 2* radius of water (if water is solvent).
If so, why smaller value is presented?
  Can the distance between closest solute atom and box cell in X direction
be consider as (69.769-56.888)/2?
  I set buffer to be 10 because I hope there is enough distance distance
between closest solute atom and box cell in simulation, but it seems there
is not 10 angstrom separate in X direction based on the box size above.I
hope that the distance between solute and box cell is not close, which
results in serious bondary effect. Is my consideration right? Anybody can
help me?
Thanks in advance.

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Received on Wed Jan 22 2003 - 04:58:53 PST
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