[AMBER] Calculating energies per residue pair, rather than per residue

From: Tue <tue.boesen.protonmail.com>
Date: Fri, 28 Jan 2022 02:09:32 +0000


I am running Amber energy calculations through MMPBSA.py, which gives me a .csv file containing the binding energy per residue. (technically it gives the energies split into various components such as Internal, van der Waals, ect.)
I was wondering whether there is any way of getting the energy per residue pair, rather than per residue - as in the interaction energy.

So for a n residue molecule I would then get an n x n energy matrix, which when summed over all columns would give the residue energy as before.

Does anyone know whether this is possible to calculate with Ambertool or any other software? I would imagine it is calculated internally in such energy calculations, but I am not sure.

Kind Regards
Tue Boesen
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Received on Thu Jan 27 2022 - 18:30:02 PST
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