AMBER: Calculating energy for specific part of system

From: Adam Pelzer <>
Date: Tue, 18 Jul 2006 15:32:34 -0700 (PDT)

Dear AMBER users,

I want to calculate the energy (potential, kinetic, or total) for a fraction of my system: one protomer in a polymer that I am simulating. This protomer is not covalently bonded to the other protomers. Is there a way to measure the energy just for this one protomer? I looked at the mm_pbsa information hoping that perhaps I could label the protomer of interest as the "ligand" or "receptor" and calculate its energy, but my understanding is that mm_pbsa would calculate the energy as though the protomer were alone in solution, rather than in its true place within the polymer (where it is not exposed to solvent on all sides). Does anyone have any suggestions on how to calculate the energy of a specific part of a system? I am interested in doing this both for minimizations and MD simulations.

Thank you very much for any advice.


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Received on Wed Jul 19 2006 - 06:07:12 PDT
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