Re: [AMBER] Amber parameters for Boron atom

From: David Case <>
Date: Sat, 19 Jan 2019 14:34:42 +0000

On Thu, Jan 17, 2019, Vincenzo Maria D'Amore wrote:

>I’m trying to set up a protein-ligand complex for MD in Amber. My ligand
>has a Boron atom. I have already optimised geometry and calculated ESP
>with Gaussian. DO you have any suggestion to parametric the ligand due to
>the fact that neither GAFF neither Amber has Boron atom type?

Not really. There is a somewhat recent discussion here:

My personal opinion is that the complexity of boron chemistry will inhibit
creation of general force fields. It makes a *lot* of difference what
kind of boron environment is in your ligand.

You might consider doing QM/MM for the ligand. You'd still have to invent
dummy MM parameters for the ligand, but that is not nearly as onerous as
trying to get the good ones you would want for an MM-only calculation.


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Received on Sat Jan 19 2019 - 07:00:02 PST
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