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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