genbox VERSION 3.3_beta_20050823

genbox -cp protein.gro -cs spc216.gro -ci insert.gro -o out.gro -p topol.top -[no]h -nice int -box vector -nmol int -try int -seed int -vdwd real -shell real

Genbox can do one of 3 things:

1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and -cp with a structure file with a box, but without atoms.

2) Solvate a solute configuration, eg. a protein, in a bath of solvent molecules. Specify -cp (solute) and -cs (solvent). The box specified in the solute coordinate file ( -cp ) is used, unless -box is set, which also centers the solute. The program editconf has more sophisticated options to change the box and center the solute. Solvent molecules are removed from the box where the distance between any atom of the solute molecule(s) and any atom of the solvent molecule is less than the sum of the VanderWaals radii of both atoms. A database ( vdwradii.dat ) of VanderWaals radii is read by the program, atoms not in the database are assigned a default distance -vdw

3) Insert a number ( -nmol ) of extra molecules ( -ci ) at random positions. The program iterates until nmol molecules have been inserted in the box. To test whether an insertion is successful the same VanderWaals criterium is used as for removal of solvent molecules. When no appropriately sized holes (holes that can hold an extra molecule) are available the program tries for -nmol * -try times before giving up. Increase -try if you have several small holes to fill.

The default solvent is Simple Point Charge water (SPC), with coordinates from $GMXLIB/spc216.gro solvents are also supported, as well as mixed solvents. The only restriction to solvent types is that a solvent molecule consists of exactly one residue. The residue information in the coordinate files is used, and should therefore be more or less consistent. In practice this means that two subsequent solvent molecules in the solvent coordinate file should have different residue number. The box of solute is built by stacking the coordinates read from the coordinate file. This means that these coordinates should be equlibrated in periodic boundary conditions to ensure a good alignment of molecules on the stacking interfaces.

The program can optionally rotate the solute molecule to align the longest molecule axis along a box edge. This way the amount of solvent molecules necessary is reduced. It should be kept in mind that this only works for short simulations, as eg. an alpha-helical peptide in solution can rotate over 90 degrees, within 500 ps. In general it is therefore better to make a more or less cubic box.

Setting -shell larger than zero will place a layer of water of the specified thickness (nm) around the solute. Hint: it is a good idea to put the protein in the center of a box first (using editconf).

Finally, genbox will optionally remove lines from your topology file in which a number of solvent molecules is already added, and adds a line with the total number of solvent molecules in your coordinate file.

-cp protein.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml

-cs spc216.gro Input, Opt., Lib. Generic structure: gro g96 pdb tpr tpb tpa xml

-ci insert.gro Input, Opt. Generic structure: gro g96 pdb tpr tpb tpa xml

-o out.gro Output Generic structure: gro g96 pdb xml

-p topol.top In/Out, Opt. Topology file

-[no]h no Print help info and quit

-nice int 19 Set the nicelevel

-box vector 0 0 0 box size

-nmol int 0 no of extra molecules to insert

-try int 10 try inserting -nmol*-try times

-seed int 1997 random generator seed

-vdwd real 0.105 default vdwaals distance

-shell real 0 thickness of optional water layer around solute

- Molecules must be whole in the initial configurations.

- At the moment -ci only works when inserting one molecule.

gromacs(7)

More information about the GROMACS suite is available in /usr/share/doc/gromacs or at <http://www.gromacs.org/>.