I have solvated a ligand molecule with water molecules within a box defined by "inside box 0. 0. 0. 33.726 33.726 33.726" in packmol. Will it be meaningful and helpful to use editconf for defining a dodecahedron box (like 'editconf -f solvated.pdb -o solvated.pdb -bt dodecahedron -d 1')?
Hiqmet Kamberaj
Waters outside the dodecahedron will normally be deleted. You may also rename the new output, e.g., -o newsolvated.pdb (.gro). Also, make sure that you are using the right periodic boundary conditions for dodecahedron box.
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