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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 with the -d option. For example,

$SCHRODINGER/run -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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