[gmx-users] Solvating dodecahedron

[Justin A. Lemkul]

shivangi nangia wrote:
> Hello All,
> 
> 
> I am trying to solvate a protein sitting in a dodecahedron using genbox.
> It gets solvated but a box of solvent is created around the protein.
> I want the protein to be sitting in a dodecahedron filed with solvent.
> 
> 
> I used the following commands:
> 
> editconf -f onlyhis.gro -bt dodecahedron -box 9 -d 1 -o dodec.gro
> genbox -cp dodec.gro -cs mix.gro -o solv.gro
> 
> 
> I have never used this utility of creating a docecahedron nor I could 
> find a way to view the dodecahedron shae in VMD.
> Am I going wrong?
> 

Nothing is wrong.  The unit cell will always be in a triclinic representation. 
You can see a dodecahedron using trjconv -pbc mol -ur compact.  Note that the 
pseudo-sphere representation is for visualization purposes only; the triclinic 
cell should be the input for any simulation.

-Justin

-- 
========================================

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

========================================