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

mu xiaojia muxiaojia2010 at gmail.com
Tue May 22 18:36:25 CEST 2012

try trjconv, maybe your reference gro/tpr file is cubic?

make sure:
trjconv -s the_dodecahedral_generated.tpr -f the_dodecahedral_generated.gro
-o your_aim.pdb

On Tue, May 22, 2012 at 9:27 AM, patrick wintrode <pat_wde2 at yahoo.com>wrote:

> 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?
> Thanks.
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