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Article ID: 451 - Last Modified: June 6, 2011

The results of the rmsdcalc script, used to perform alignment and rmsd calculations, are not consistent with what I obtained from the Superposition tool in Maestro, and I think that the result from the Maestro tool is more reasonable. Is it possible to use the "superposition" utility from the command line?

The reason for the discrepancy is that rmsdcalc is mostly used on conformers, so it expects the exact same atom numbering and connectivity. A slight variation (for example 180-degree phenyl ring rotation) can have a dramatic effect on RMSD. If you print out the usage info with:

$SCHRODINGER/utilities/rmsdcalc -h

there is a note that "RMSD cannot be computed between two structures unless they have the same connectivity." It also prints various options of which one is:

-renumber : Investigate alternate atom numbering schemes to identify 180-degree ring twists and other symmetry operations that may reduce RMSD. Use caution in combination with explicit hydrogen treatment since there may be a very large number of ways to renumber hydrogens.

There is another option for calculating RMSD via a Python script,, which is available from our Script Center. Running it with the following command:

$SCHRODINGER/run filename1.mae filename2.maegz -m -a "all"

should also give the same result. Try the "-use_neutral_scaffold" option for superimposing all heavy atoms.

Keywords: RMSD , superposition , discrepancy , rmsdcalc,, Maestro

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