Re: [AMBER] principal component analysis

From: Daniel Roe <>
Date: Mon, 11 May 2015 13:55:38 -0600


>From your description it's not exactly clear to me what you are trying
to accomplish. I think it would be better if you said exactly what
programs you're using (and the version) as well as the exact input you
used. What is meant by 'departure RX structure'?


On Mon, May 11, 2015 at 3:27 AM, abdennour braka
<> wrote:
> Dear Amber users,
> I have sampled a protein conformations with REMD to use frames in a
> multi conformational screening.
> To compare the results of the MD with RX structures, I have added the RX
> to the trajectory, aligned all conformations on the same reference and
> performed a PCA on the heavy atoms of the active site.
> However, I found that in the 3 first PC (PC1, PC2, PC3) my departure RX
> structure of the MD is far from the first frame of the MD.
> Do you have any idea why I find this difference and if there is another
> way to compare RX conformations with MD frames.
> Thank you for any replies.
> //
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon May 11 2015 - 13:00:03 PDT
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