Re: [AMBER] drug including B atom

From: David A Case via AMBER <>
Date: Thu, 16 Feb 2023 09:07:50 -0500

On Thu, Feb 16, 2023, laura zhang via AMBER wrote:
>I am working on a drug molecule which has a B atom. I got the following
>error message when trying to generate forcefield parameters for this
>molecule using antechamber.

GAFF does not support boron. I'm a little surprised that acdoctor did not
make a clear report of that, but it's hard to be sure without seeing your
input file.

You can look into mgdx or parmfit to help generate a force field by hand,
using (probably) some quantum calculations as input. It's certainly worth a
Google search to see if compounds like yours have been fit to simple force
fields before.


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Received on Thu Feb 16 2023 - 06:30:03 PST
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