Drear all,

I would like to make water-box/ions for my protein-complex system. Could make it with automated feature in packmol:

solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -i pack.inp -o solvated.pdb

but in I have tried to make it manually with both cube and box shaped water and the protein is oriented out of box/edge side. have used these keywords:

#

# Protein solvated by water and ions

#

tolerance 2.0

structure protein.pdb

number 1

center

fixed 0. 0. 0. 0. 0. 0.

end structure

structure water.pdb

number 16500

inside cube 0. 0. 0. 115.

end structure

structure SOD.pdb

number 30

inside cube 0. 0. 0. 115.

end structure

output solvprotein.pdb

Any suggestion would be appreciated...

Cheers

Zahra