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

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