[gmx-users] sphere around a protein

Justin A. Lemkul jalemkul at vt.edu
Sun May 8 23:12:33 CEST 2011

shivangi nangia wrote:
> 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.

And why not?

genbox -cp protein.gro -cs sphere.gro

should do exactly what you want, provided the sphere is large enough for the 


> Is there another feasible route to get to my desired configuration of 
> the system ?
> Thanks in advance
> Best,
> SN


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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