Re: [AMBER] Regarding cosine content calculation in AMBER

From: Pratul Agarwal <>
Date: Tue, 30 Apr 2019 16:46:56 +0000

To the best of my knowledge, such a functionality is not implemented in cpptraj. Others can correct me if I am wrong. Probably easiest to convert to GROMACS trajectory, and use gmx analyze.

Also, are you trying to perform this analysis for a protein? If you are, be careful. The assumption for such an analysis seems to be "This is useful for principal components obtained from covariance analysis, since the principal components of random diffusion are pure cosines."

Protein motions are not always harmonic and definitely are not similar to random diffusion. Exercise caution, if you are trying to use this as a criterion for evaluating the convergence of your MD trajectory.

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

On 4/30/2019 12:14 PM, Rajarshi Roy wrote:

Yes. Please check this acs paper and you will get that data in their
 Exploring Protein Stability by Comparative Molecular DynamicsSimulations
of Homologous Hyperthermophilic, Mesophilic, andPsychrophilic Proteins
and also you can check this scientific report paper
Alanine mutation of the catalyticsites of Pantothenate Synthetasecauses
distinct conformationalchanges in the ATP binding region

On Tue, Apr 30, 2019 at 9:27 PM Pratul Agarwal <><>

Do you have a reference to a paper, where such a cosine calculation has
been performed?

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

On 4/30/2019 11:47 AM, Rajarshi Roy wrote:

No Sir. I am talking about the cosine content of the pca projection (not
dihedral pca), which is also a measure of convergence of the md simulation.

On Tue, Apr 30, 2019 at 6:47 PM Daniel Roe <<>

<><> wrote:


By "cosine content" do you mean performing principal component
analysis in dihedral space instead of Cartesian? If so, then yes
cpptraj can do this. There's even an example in the manual - see
'Dihedral covariance matrix calculation' in the 'Analysis Examples'
section of the cpptraj part of the Amber manual.

If you want to convert to a Gromacs format, use either the command
line or 'trajout' and convert to 'trr' or 'xtc' format (see manual for


On Tue, Apr 30, 2019 at 1:23 AM Rajarshi Roy <<>



Dear AMBER users and Development Team,
I have a query on principal component analysis using cpptraj. Does


calculate cosine content of the PC? If so, Can we print that data in a
file? Can it be possible in new ambertools? As we know it can be done in
gromacs, so which is the best and quick way to convert amber trajectory


gromacs trajectory?

Thank you in advance.

*with regards*
*Rajarshi Roy*
*PhD Research Scholar*
*Biosciences and Biomedical Engineering*
*Indian Institute of Technology, Indore*
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Received on Tue Apr 30 2019 - 10:00:01 PDT
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