Knowledge Base

Article ID: 825 - Last Modified:

For a set of conformers, is it possible to generate an RMSD matrix with the rmsd containing the rmsd between each pair of conformations?

You can use the python script rmsd.py with the -d option. For example,

$SCHRODINGER/run rmsd.py -a "not atom.ele H" -d matrix.txt conformer-file conformer-file

In the command above, the ASL expression compares heavy-atoms only.

Keywords: conformers, rmsd

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 help@schrodinger.com.
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