[gmx-users] Solvating dodecahedron

[shivangi nangia]

Hello All,


I am trying to solvate a protein sitting in a dodecahedron using genbox.
It gets solvated but a box of solvent is created around the protein.
I want the protein to be sitting in a dodecahedron filed with solvent.


I used the following commands:

editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro
genbox -cp dodec.gro -cs mix.gro -o solv.gro


I have never used this utility of creating a docecahedron nor I could find a
way to view the dodecahedron shae in VMD.
Am I going wrong?


Thanks,
SN
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