Re: [AMBER] Estimating protein-protein interactions

From: David A Case <>
Date: Wed, 30 Jun 2021 09:01:29 -0400

On Mon, Jun 28, 2021, Matthew Guberman-Pfeffer wrote:

>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?

It's not clear what you are computing, or exactly how. How do the numbers
you get compare to the values that are printed in the mdout file? Are you
only computing a subset of the LJ interactions?


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Received on Wed Jun 30 2021 - 06:30:03 PDT
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