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
protein.
-Justin
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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