AMBER Archive (2006)

Subject: AMBER: iso command and a cubic box

From: Patricia Hunt (p.hunt_at_imperial.ac.uk)
Date: Wed Jul 12 2006 - 02:03:03 CDT

Hi,

        I'm trying to understand AMBER 9.0 solvate box command, I want a
perfectly cubic box, however the iso command in solvate box doesn't
seem to be giving me that.

Request:
"solvatebox ion SPCBOX 10 iso 0.8"

Output:
Reading MOLECULE named ION
   Solute vdw bounding box: 3.896 3.896 3.896
   Total bounding box for atom centers: 23.896 23.896 23.896
       (box expansion for 'iso' is 0.0%)
   Solvent unit box: 18.774 18.774 18.774
   Volume: 20214.665 A^3
   Total mass 7115.738 amu, Density 0.585 g/cc
   Added 393 residues.

Which are the PBC used in AMBER?
When I look in the prmtop file and search for BOX I get:
%FLAG BOX_DIMENSIONS
%FORMAT(5E16.8)
   9.00000000E+01 2.71882150E+01 2.71884770E+01 2.73464510E+01

And in the inpcrd file is (last line)
27.1882150 27.1884770 27.3464510 90.0000000 90.0000000 90.0000000

        Which is not cubic. How can I enforce a cubic box?
        Is it safe to just manually change these dimensions? Will it muck
other things up?

        Many thanks,

                        Tricia.

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