The Packmol distribution includes the solvate.tcl script, which is used to solvate large molecules, usually proteins, with water and ions (Na+ and Cl-). Given the PDB file of the biomolecule, just run the script with:
And the script will create a input file for packmol called packmol_input.inp. With this file, run Packmol with:
packmol < packmol_input.inp
And your large molecule will be solvated by a shell of 15. Angs. of water, and ions to keep the system neutral and a physiological NaCl concentration of 0.16M. The script usually makes reasonable choices for every parameter (number of water molecules, number of ions, etc.), but these may be controlled manually with additional options, as described below:
solvate.tcl structure.pdb -noions
solvate.tcl structure.pdb -shell 15. -charge +5 -density 1.0 -i pack.inp -o solvated.pdb
Where: structure.pdb is the pdb file to be solvated (usually a protein)
"15." is the size of the solvation shell. This is an optional parameter. If not set, 15. will be used.
"-charge +5" is the total charge of the system, to be neutralized. This is also and optional parameter, if not used, the package considers histidine residues as neutral, Arg and Lys as +1 and Glu and Asp as -1. The Na+ and Cl- concentrations are set the closest possible to 0.16M, approximately the physiological concentration. Alternatively, use the -noions to not add any ions, just water.
1.0 is the desired density. Optional. If not set, the density will be set to 1.0 g/ml.
solvated.pdb: is the (optional) name for the solvated system output file. If this argument is not provided, it will be the default solvated.pdb file.
pack.inp: is the (optional) name for the packmol input file that will be generated. If not provided, packmol_input.inp will be used.
All these options are output when running the "solvate.tcl" script without any parameter. The script also outputs the size of the box and the suggested periodic boundary condition dimensions to be used.
obtained from Packmol user-guide (http://www.ime.unicamp.br/~martinez/packmol/userguide.shtml)