[AMBER] Cpptraj: Move origin to specific coordinates

From: Waldner, Birgit <Birgit.Waldner.uibk.ac.at>
Date: Tue, 21 Oct 2014 13:09:31 +0000

Dear Amber users,

I would like to achieve the following task using cpptraj, but can't find a straightforward way to do all of it directly in cpptraj:

1. Calculate a vector from the center of mass of the whole protein (centered at 0 0 0) to the center of mass of the residues specified in a second mask.
2. Elongate the vector by 10-20%.
3. Set the origin to the coordinates stored in the elongated vector.
And all this for each frame of the trajectory.
Basically I want to move the origin 10-20% away from the residues specified in the second mask, but in the direction of the vector from the center of mass of the protein to the center of mass of the atoms in the second mask.
I can calculate the vector in step 1, but then I can't find in the manual how to perform the actions of step 2 and step 3 in cpptraj.

Does anyone know how or if this can all be done in cpptraj? Could the "scale" command help? Is there an option to multiply a vector with a matrix or scalar in cpptraj?

Thank you very much for your help, best regards,

Birgit Waldner

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Received on Tue Oct 21 2014 - 06:30:03 PDT
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