Re: [AMBER] PCA calculation projection

From: Pratul Agarwal <>
Date: Wed, 11 Sep 2019 12:59:51 +0000


What did trajectory visualization show? Did you see some part of your protein moving more than others?

These kinds of results could be real. Protein motions can be anharmonic, which certainly seems to be the case for your protein. This is indicated by the projection on first PCA vector showing additional peak(s) with small populations. Please remember PCA is a quasi-harmonic approximation of the motions (fitting a second order/harmonic curve). If there are multiple peaks along a projection, it implies that there are multiple wells along the same eigenvector, in such cases PCA may not be the best technique to obtain accurate results.


Pratul K. Agarwal, Ph.D.
(Editorial Board Member: PLoS ONE, Microbial Cell Factories)

On 9/11/2019 6:22 AM, Aashish Bhatt wrote:

Dear Sir/Ma'am

I am interested in PCA calculation for the my wild type protein. I had gone
through the tutorial (
pca/) and prepared this cpptraj script.

My problem is that in 2D PC1 and PC2 image they have coming -250 to 70. I
am suspect that the projection on X axis is very negative.
Could you give me some comment why it showing negative or something i am
doing is wrong.

Best Regards


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Received on Wed Sep 11 2019 - 06:30:05 PDT
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