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

From: Matthew Guberman-Pfeffer <>
Date: Thu, 27 Jan 2022 22:34:24 -0500

Have you looked at the linear interaction energy (LIE) approach in CPPTRAJ?
It returns the interaction energy between any two masks.
You can loop over all residue pairs for a given residue of interest and sum up the energies.


> On Jan 27, 2022, at 9:09 PM, Tue <> wrote:
> *Message sent from a system outside of UConn.*
> Hi
> I am running Amber energy calculations through, 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 - 20:00:02 PST
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