Article ID: 623 - Last Modified: May 16, 2013
How can I calculate the volume of a molecule?
For ligand-like molecular volumes, try the script volume_calc.py, which is available from the Script Center and is included in the software distribution. The script takes a Maestro file as input and computes the volume of each structure. The volume is calculated numerically on a grid using a set of atomic radii (Bondi or Pauling). The unit of volume is Å3, and the volume is calculated using the non-hydrogen atoms in the molecule. The usage is:
$SCHRODINGER/run volume_calc.py -imae filename.mae
Another option is to use the utility phase_volCalc, which calculates the volume overlap of the structures in one Maestro file with the structures in another. If you use the same structures for both, the volumes will appear in the CSV output as the diagonal elements of the volume overlap matrix. By default, the van der Waals radii of the atoms are used and hydrogens are not included, but the utility gives control over the atomic radii, the grid spacing, and the inclusion of hydrogens.
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