[gmx-users] sphere around a protein

shivangi nangia shivangi.nangia at gmail.com
Sun May 8 22:13:33 CEST 2011

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

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