Hi,
On Mon, Oct 25, 2021 at 4:21 PM Thomas Cheatham <tec3.utah.edu> wrote:
>
> In a final note, regarding chemically equivalent states of a molecule, if
> not addressed, can lead to artificially higher RMSD values - an example is
> phenylalanine where the side chain flipped state (rotated 180 deg) is
> chemically equivalent, but atom names do not match so higher RMSD. CPPTRAJ
> has the capability to correct for this...
For posterity, the command is ‘symmrmsd’ for symmetry-corrected RMSD. You
can also use symmetry corrected RMSD in cluster analysis.
-Dan
>
>
> --tec3
>
>
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Received on Thu Nov 11 2021 - 06:30:02 PST
