Re: [AMBER] Regarding cosine content calculation in AMBER

From: Daniel Roe <>
Date: Tue, 30 Apr 2019 09:16:45 -0400


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 <> wrote:
> Dear AMBER users and Development Team,
> I have a query on principal component analysis using cpptraj. Does cpptraj
> 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 to
> gromacs trajectory?
> Thank you in advance.
> --
> *with regards*
> *Rajarshi Roy*
> *PhD Research Scholar*
> *Biosciences and Biomedical Engineering*
> *Indian Institute of Technology, Indore*
> *India*
> _______________________________________________
> AMBER mailing list

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Received on Tue Apr 30 2019 - 06:30:03 PDT
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