[gmx-users] Octahderal box

[Joanne Hanna]

Hi

I am having some difficulties with a truncated octahedron box.

I have made the box using:

editconf -f ENZ.pdb -d 1.0 -bt octahedron -o box.gro

viewing this in rasmol with the unitcell gives me what looks like a triclinic box.

After solvating this using:

genbox -cp box.gro -cs spc216.gro -o solv.gro

and viewing this in vmd i get what appears to be a cubic box with the enzyme not centered and sticking out of the solvated box.

Does anyone have any ideas where i am going wrong?

The output from the editconf is:

Read 5213 atoms
Volume: 309.565 nm^3, corresponds to roughly 139300 electrons
No velocities found
    system size :  6.557  7.485  6.307 (nm)
    diameter    :  7.941               (nm)
    center      :  3.329 10.051  3.262 (nm)
    box vectors :  6.557  7.485  6.307 (nm)
    box angles  :  90.00  90.00  90.00 (degrees)
    box volume  : 309.56               (nm^3)
    shift       :  1.642 -3.022  0.796 (nm)
new center      :  4.970  7.029  4.058 (nm)
new box vectors :  9.941  9.941  9.941 (nm)
new box angles  :  70.53 109.47  70.53 (degrees)
new box volume  : 756.24               (nm^3)

gcq#231: "Let's Go Hang Out In a Mall" (LIVE)

and the bottom of the *.gro looks like:

  514PHE    HE1 5206   7.728   5.684   1.408
  514PHE    CE2 5207   7.795   5.899   1.651
  514PHE    HE2 5208   7.756   5.936   1.735
  514PHE     CZ 5209   7.724   5.804   1.578
  514PHE     HZ 5210   7.635   5.773   1.609
  514PHE      C 5211   8.091   5.970   1.193
  514PHE     O1 5212   7.983   5.994   1.114
  514PHE     O2 5213   8.194   5.886   1.163
   9.94094   9.37241   8.11675   0.00000   0.00000   3.31365   0.00000  -3.31365   4.68621

Any advice would be greatly appreciated.

Thanks

Jo



Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL

J.F.Hanna at warwick.ac.uk