Re: [AMBER] Rodrigues' rotation about a specified vector

From: David A Case <>
Date: Tue, 10 Aug 2021 15:09:48 -0400

On Wed, Aug 11, 2021, Vaibhav Dixit wrote:

>I am trying to translate a specific atom to the origin and then perform
>Rodrigues' rotation about a specific axis (vector) by a specific angle.
>Thus am curious to know if this can be performed using ambertools?
>Also it would be great if one could directly use a pdb for this thus
>avoiding the need to create parameter and topology file.

This is exactly the sort of thing NAB was originally designed to do.
Grab the Amber16 Reference manual (from,
and look at Sections 36.11 and 37.15. In brief, you would write a script
something like this:

     getpdb (load a pdb file)
     trans4 (to translate some atom to the origin)
     rot4 (to rotate about some vector by some amount)
     trans4 (optional, to undo the first translation)
     putpdb (output the modified coordinates)

[Note: the NAB code is still in AmberTools21, but one has to visit the old
Manual to get the instructions.]

...good luck....dac

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Received on Tue Aug 10 2021 - 12:30:02 PDT
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