Re: [AMBER] Interaction energy by MM-PBSA for a superantigen with important Zn(II) center

From: David A Case <>
Date: Sat, 20 Feb 2021 09:24:25 -0500

On Fri, Feb 19, 2021, SATYAJIT KHATUA wrote:
>I am calculating the protein-protein interaction energy for a superantigen
>system. I am using MM-PBSA for that estimation. But, the problem is that I
>have an important ZN (II) center through which the two fragment interacts.

If the zinc bridges the two proteins, you essentially have a covalent
connection, and it will be hard to get binding energies. Think carefully
about what reactions you are studying, what experimental data you might
have, and what you would do with the result.

>When I have subjected the trajectory to binding energy estimation, it
>couldn't able to detect the radius for the metal center.

Look at at the "radiopt" option, which will use the radii in the prmtop


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Received on Sat Feb 20 2021 - 07:00:04 PST
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