Re: [AMBER] Distance of every c alpha in a protein to every other c alpha

From: Daniel Roe <>
Date: Tue, 19 Jan 2021 09:46:07 -0500


Probably the most straightforward way is to calculate a matrix of the
average distance between all CA atoms using the 'matrix' action with
'dist' keyword. Something like:

parm myparm.parm7
matrix dist .CA out dist.gnu header

In this case I'm writing out a gnuplot-readable file, but you can
change the format to a "plain" data file by using '.dat' instead of


On Mon, Jan 18, 2021 at 12:51 AM Jenny 148 <> wrote:
> Dear all,
> Is there a way to calculate the distance of every c alpha atoms of a
> protein to every other c alpha of the same plot. This to find the largest
> deviation from a scatter plot for a comparative study of the changes due to
> a modification in the protein. Kindly help.
> --
> Jenny R.S
> _______________________________________________
> AMBER mailing list

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Received on Tue Jan 19 2021 - 07:00:02 PST
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