Example 4: Using a truncated octahedral box

A truncated octahedron is a space-filling solid that can mimic an infinite system in MD simulations when periodic boundary conditions are applied. It can be constructed from a cube by slicing off the corners of a cube with a plane that makes a perpendicular cut through the diagonal of the cube halfway between the center and the corner of the cube. Its shape is much closer to spherical than a cube is and solute can be assured to be a specified distance away from image solute molecules even if they rotate. It is more efficient than a cube that would provide the same assurance because there are no corners. Since it is space filling, and all space filling shapes can be mapped to a triclinic unit cell that reproduces the same periodic system, AMBER uses the triclinc representation in its simulation of truncated-octahedral systems.

The example provided makes a solvated periodic system with bpti as the solute and water as solvent in a truncated octahedral shape and its related triclinic shape. Both represent the same system.

It takes two steps to create the input coordinates and the prmtop file for runing sander with truncated octahedral (TO) periodic boundary conditions (PBC). First, one creates a solvated system in a large cubic box. Second, the water is stripped off to make the truncated-octahedral system and write out the coordinates and prmtop file.

Use LEaP to make a large cube. Start tleap or xleap

% tleap

> pti = loadpdb 1bpi.pdb

This command will load the pdb into leap and add hydrogens and call the unit "pti".
> solvatebox pti WATBOX216 20. 1.
The unit, pti, is solvated with water using the equilibrated water box WATBOX216. Enough WATBOX's are added to make the solvent extend at least 20 A past the solute in each of the 6 directions: + and - for x, y, and z. The last argument specifies that no solvent molecule can be closer than 1 A to the solute.
> saveamberparm pti b_cube.top b_cube.crd
> quit
The unit will be saved as parm topology and coordinate files for running in sander.

Use ptraj Cut down to a truncated octahedral shape.

-----------Comments------------------ input/commands -------------------
start ptraj with the cubic prmtop |
| % ptraj b_cube.top
Read in cubic coordinates | trajin b_cube.crd
Write TO coordinates to file | trajout b_oct.crd restart
in restart format |
Transform coordinates to TO PBC | truncoct :1-58 10. prmtop b_oct.top
-solute is in residues 1 to 58 |
-buffer between solute and |
sides of TO is 10. A |
-write a prmtop file called |
b_oct.top |
End the input and do the work |
| %
The resulting coordinate file is b_oct.crd.1 which should be renamed to b_oct.crd by convention. Sander can now be used as
% sander -p b_oct.top -c b_oct.crd [... other arguments ]
A sample set of scripts is provided with the master script "Run" in the $AMBERHOME/examples/TO_sample subdirectory. When it is finished, one can check the output files from the sander runs to make sure that the energies match between the different starting shapes, showing that the inaging is correct. One can also view the pdb files produced to see what the two different but equivalent shapes look like. If the TO shape is desired as output from sander, be sure to use "iwrap=1," in the &cntrl namelist of sander. Alternatively, you can use ptraj to convert "unwrapped" coordinates into a shape that is that of a truncated octahedron.


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Updated on January 5, 2000. Comments to case@scripps.edu