AMBER Archive (2006)

Subject: AMBER: iso command and a cubic box

From: Patricia Hunt (
Date: Wed Jul 12 2006 - 02:03:03 CDT


        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.

"solvatebox ion SPCBOX 10 iso 0.8"

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:
   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,


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