[AMBER] Estimating protein-protein interactions

From: Matthew Guberman-Pfeffer <matthew.guberman-pfeffer.uconn.edu>
Date: Mon, 28 Jun 2021 22:21:44 -0400

Dear Amber Community,

I am trying to compute how the stability of a protein-protein interface changes with protonation of the acidic groups within a 10 Å distance of the interface. I’ve computed the non-bonded interactions for MD snapshots using either the linear interaction method with some dielectric constant specified (4 or 80) or using esander. One aspect that confuses me is that the VDW energies are positive. I was expecting strongly negative values. Is there just a sign convention I’m missing?

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Received on Mon Jun 28 2021 - 19:30:02 PDT
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