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From: Tue <tue.boesen.protonmail.com>

Date: Fri, 28 Jan 2022 02:09:32 +0000

Hi

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

Date: Fri, 28 Jan 2022 02:09:32 +0000

Hi

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

_______________________________________________

AMBER mailing list

AMBER.ambermd.org

http://lists.ambermd.org/mailman/listinfo/amber

Received on Thu Jan 27 2022 - 18:30:02 PST

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