Hi Justin and other gmx-users, I want to make a sphere around a protein (5nm).with Li ions and anions.
Justin, as you had suggested to use genbox -shell option, I tried using it but i realized that since my protein is a long tube like structure, the shell option generated a cyclinder around the protein. The solvent around the protein is 1:1 water-methanol (pre-prepared mixture n a gro file) If I try to start with a ion and solvate it with my solvent (1:1 water methanol) using -shell option, I do get a sphere but then I am unable to insert the protein in the system. Is there another feasible route to get to my desired configuration of the system ? Thanks in advance Best, SN
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