AMBER Archive (2003)

Subject: How much is minimum distance

From: pu xuemei (pxmscu_at_hotmail.com)
Date: Fri Jan 24 2003 - 01:11:29 CST

Dear Amber user
  Thanks everyone who help me before.
 Now I still have one problem. 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.

  Because I hope that the distance between closest solute atom and box cell
is 10.0 angstrom,I set buffer as 10.0 angstrom. Based on the solvate above,
we know the final box size is 69.769 67.795 67.795 (smaller than "total
bounding box for atom centers 76.888 65.091 66.347" in x direction). I want
to know if the distance between closest solute atom and box cell still keep
in 10.0 angstrom in x y z dimension of final box size? Do Xleap determine
the final box size based on buffer value (such as 10.0 angstrom)? or
direction of solute molecule in final box size is different from that in
original "solute vdw bounding box"(or "Total bounding box for atom
centers")?
  The question has been confused me so that I am not sure what close the
separate between the solute molecule and box cell is after MD
simulation.Anybody can help me?
By the way, is there Shake constrain only for solvent molecules in Amber 6?

Thanks in advance.
pxm

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