Xplor-NIH home Documentation |
Next: Patching the Molecular Structure Up: Generating the Molecular Structure Previous: Example: Water Molecules
Example: Solvation of a Solute
The atom selection feature in X-PLOR can be used to
solvate a solute, such as protein or nucleic acid. Suppose the
user has set up coordinates and molecular structure files for the solute
(“solute.pdb" and “solute.psf") and
for a box of water
(“water.pdb" and “water.psf" with SEGId “WAT")
that is large enough to enclose the solute. The
following X-PLOR script will create a composite coordinate and
molecular structure file (“overlay.pdb" and “overlay.psf")
deleting all waters that penetrate the
protein:
structure @solute.psf end coordinates @solute.pdb structure @water.psf end coordinates @water.pdb delete selection= ( byres ( segid "WAT" and ( ( not segid "WAT" and not ( hydrogen ) ) around 2.6 ) )) end write structure output=overlay.psf end write coordinates output=overlay.pdb endIf the box of water molecules is not large enough, it can be made larger by duplicating and translating the original box (cf. Section 3.10).
Xplor-NIH 2024-09-13