can you be more specific about the problem? calculating the RMSD should not
depend on an insertion.
you can choose any residue range that you want using an atom mask in the
rmsd command.
but - are you trying to compare the one with the insertion to the one
without the insertion? that would be more complex, but still possible.
On Fri, Mar 29, 2024 at 12:38 PM Colin Pierce via AMBER <amber.ambermd.org>
wrote:
> Hello,
> I need to calculate the RMSD of an enzyme variant that contains a
> roughly 100 residue domain insertion. I’ve searched extensively and have
> been unable to find a way to do this. It seems that it may be possible in
> Amber22 by renaming the residues in cpptraj, however only Amber20 is
> supported in the HPC at my institution.
>
> Is there a way to exclude specific residues in the protein of interest
> from the RMSD comparison? I would like to exclude only those residues in
> the domain insertion so that I can assess the effects of the insertion on
> the rest of the protein.
>
> Thank you,
>
> Colin Pierce
> Postdoctoral Associate
> University of Minnesota
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Received on Fri Mar 29 2024 - 10:00:02 PDT
