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_w...@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. > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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