Re: [AMBER] CPPTRAJ, PCA, Effect of Mutation

From: Daniel Roe via AMBER <>
Date: Mon, 6 Feb 2023 08:13:38 -0500


You'll need to restrict the calculation of your combined covariance
matrix to only atoms that are common to the two proteins. Probably the
easiest way to do that is to e.g. select only the backbone atoms or
just the alpha carbons.


On Tue, Jan 31, 2023 at 11:37 AM Matthew Guberman-Pfeffer via AMBER
<> wrote:
> Dear AMBER Community,
> How can I modified the example Principle Component Analysis script given at the below link to compare the PCs for a protein both and after a mutation?
> Best,
> Matthew
> _______________________________________________
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Received on Mon Feb 06 2023 - 05:30:02 PST
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