Re: [AMBER] huge difference in GB and PB energies calculated with

From: David A Case <>
Date: Fri, 6 Jul 2018 08:29:57 -0400

On Fri, Jul 06, 2018, Charles Mariasoosai wrote:

> there is a huge difference between the GB and PB energy values I have
> calculated for the same trajectory
> My system consists of protein-cofactor-inhibitor-4 zinc atoms.

I'm not too surprised: parameters for GB models were developed and tested for
"ordinary" proteins, and not for systems with divalent metal ions. The
electrostatic contributions of the latter are large, and likely to be
represented differently with different approaches.

Although I looked at this problem many years ago, I've not followed more
recent efforts to deal with divalent metal ions in implicit solvent;
maybe others on the list can chime in with suggestions. The "best" approach
(if there is one) probably depends a lot of the coordination geometry you


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Received on Fri Jul 06 2018 - 06:00:04 PDT
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