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