Generate custom box with packmol¶

This tutorial explains how to generate a box (.pdb file) with different species (e.g. a solute and a solvent mixture).

Lets assume we want to generate a cubic box (30x30x30 Angstroms) containing a solute molecule in its center and surrounded by a mixture of two different molecules (e.g. water and ethanol).

Generate a .pdb file for the individual species

(solute.pdb, solvent1.pdb, and solvent2.pdb). This can be done with chimera using an .xyz file.

Note

Make sure the molecules have different residue names in the .pdb files. Lets say SLU, SV1, and SV2.

Create an input file (packmol.inp) for packmol which will

generate a .pdb file for the whole solvated system (system.pdb).

packmol.inp:

# All atoms from diferent molecules will be at least 2.0 Angstroms apart
tolerance 2.0

# The type of the files will be pdb
filetype pdb

# The name of the output file
output system.pdb

# put the COM of the solute at the center of the box
structure solute.pdb
  number 1
  fixed 15. 15. 15. 0. 0. 0.
  centerofmass
end structure

# add first type of solvent molecules
structure solvent1.pdb
  number 100
  inside cube 0. 0. 0. 30
end structure

# add second type of solvent molecules
structure solvent2.pdb
  number 100
  inside cube 0. 0. 0. 30
end structure

Note

Be sure to modify the dimension of the box, the number of molecules to add, and the file names to your convenience.

Run packmol:
```
./pathto/packmol < packmol.inp
```

If you have put to many molecules in the box, packmol might fail to converge. For more information, check the packmol documentation.