Re: [AMBER] PCA multiple trajectories for mutants and wild type

From: Daniel Roe <>
Date: Thu, 12 Jul 2018 17:12:52 -0500


On Wed, Jul 11, 2018 at 6:48 AM Stejskal, Lenka <>

> Dear Amber users,
> I am trying to compare multiple trajectories of either wild type and a few
> mutant of the protein to compare differences in their dynamics. I have
> several ideas how to do this and any experience/ideas would be appreciated.
> I create the matrix based on all trajectories and project the 1st and 2nd
> PC onto individual trajectories to see a difference in the occupied phase
> space. Alternatively, as I am trying to compare the mutants to the wild
> type, I could create the matrix based just on the wild type and project
> trajectories of the mutants on these eigenvectors. I believe this might be
> a better measure.

The first method you mention is fine and in fact had been used as a measure
of convergence between independent trajectories. See e.g.
  . Just remember if you are comparing a mutant and wildtype use only the
atoms they have in common.

> I am however making an assumption that the motion is comparable. Could
> this be an issue? Is there any way I can confirm this?
> I will also calculate the eigenvectors for each trajectory individually.
> Is there a way to compare how similar these are?

Sure - you could calculate the root mean square inner product of the
eigenvectors (cpptraj command ‘modes rmsip’). See the manual for full

Hope this helps,


> Thank you very much for your help!
> Lenka
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Received on Thu Jul 12 2018 - 15:30:01 PDT
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