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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Received on Thu Jul 13 2006 - 16:34:48 PDT
