[gmx-users] problem with solvent box in gromacs 4.5.4

patrick wintrode pat_wde2 at yahoo.com
Tue May 22 16:27:23 CEST 2012

After generating my protein .gro and .top files and doing the initial energy minimization, I used the following series of commands:

editconf -f protein-vacuum.gro -o protein-PBC.gro -bt dodecahedron -d 1.2

genbox -cp protein-PBC.gro -cs spc216.gro -p protein.top -o protein-water.gro

I then use editconf to convert protein-water.gro to a pdb file. When I open this
file in PyMol, the water box is cubic rather than dodecahedral.

Has any one else encountered this?

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