Re: [AMBER] Boron containing molecules in GAFF

From: Brian Radak <>
Date: Wed, 4 Aug 2021 12:41:40 -0400

Thanks Dave. A QM/MM sanity check was actually one of the first things we
thought of too. Time for us to try out QUICK!

On Wed, Aug 4, 2021, 11:20 AM David A Case <> wrote:

> On Tue, Aug 03, 2021, Brian Radak wrote:
> >Does anyone have experience with or know the relevant literature on
> >simulations of drug-like molecules containing boron? Are these at all
> >covered by GAFF? I'm specifically thinking about ring systems containing
> >boron with a neutral formal charge and an empty sp3 orbital (something
> >tells me this is challenging for an atom centered ESP charge model).
> Boron bonding and conformational analysis is a unique topic, since
> organo-boron compounds have unique properties. There is no coverage of
> boron in GAFF. A quick Google search shows force fields for partiular
> types
> of boron compounds, but nothing pops up that looks very general.
> Handling the ligand with QM/MM would be one possibility.
> As usual, I'm hoping that others on the list who know more than I do will
> chime in here.
> ....dac
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Received on Wed Aug 04 2021 - 10:00:03 PDT
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