Knowledge Base

Article ID: 623 - Last Modified:

How can I calculate the volume of a molecule?

For ligand-like molecular volumes, try the script, which is available 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 -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.

Back to Search Results

Was this information helpful?

What can we do to improve this information?

To ask a question or get help, please submit a support ticket or email us at
Knowledge Base Search

Type the words or phrases on which you would like to search, or click here to view a list of all
Knowledge Base articles