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
> pti = loadpdb 1bpi.pdb
Use ptraj Cut down to a truncated octahedral shape.
b_oct.crd.1which should be renamed to
b_oct.crdby convention. Sander can now be used as
$AMBERHOME/examples/TO_samplesubdirectory. 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.