AMBER Archive (2007)

Subject: AMBER: setting dimensions of truncated octahedron

From: Lillian chong (ltchong_at_pitt.edu)
Date: Sat Aug 04 2007 - 15:34:59 CDT

Dear all,

I would like to solvate two different peptide conformations with truncated
octahedral boxes of water that are of the same dimensions. Can anyone
suggest a good way to specify the dimensions of an isotropic truncated
octahedron?

In leap, when I try "solvateoct model TIP3PBOX {10 10 10 10})", I get the
following error: "solvateOct: 'iso' requires a single clearance value."
When I add the "aniso" option ("solvateoct model TIP3PBOX {10 10 10 10}
aniso"), I get the following, which does not give me an isotropic truncated
octahedron even though I've specified equal x, y, and z dimensions:

Scaling up box by a factor of 1.421552 to meet diagonal cut criterion
  Solute vdw bounding box: 23.884 20.817 22.394
  Total bounding box for atom centers: 52.315 49.248 50.825
  Solvent unit box: 18.774 18.774 18.774
  Total vdw box size: 55.090 52.317 53.672 angstroms.
  Volume: 119079.311 A^3 (oct)
  Total mass 34902.380 amu, Density 0.487 g/cc
  Added 1846 residues.

Is there something that I'm missing in the syntax for the solvateOct
command?

Thanks in advance!
Lillian

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