Re: [AMBER] antechamber assigns DU as atom type for nitrogen

From: David A Case <>
Date: Sat, 23 Jan 2021 17:23:53 -0500

On Sat, Jan 16, 2021, nguerin wrote:
>I'm trying to create a forcefield modification file for dabrafenib, a
>kinase inhibitor. When dabrafenib interacts with its partner, the
>hydrogen on N40 is abstracted away. dabrafenib.pdb contains the
>dabrafenib without the hydrogen.
>I run antechamber (from ambertools 20) on the molecule as follows:
>antechamber -i dabrafenib.pdb -fi pdb -o dabrafenib.prepi -fo prepi -c
>bcc -at amber -nc -1 -pf -dr
>which produces the the file dabrafenib.prepi (attached).
>The issue is that N40's atom type in the prepi file is DU, and DU as
>this atom type doesn't allow me to generate a forcefield modification

Sorry to be slow in getting back to you. You asked for Amber atom types,
but that is designed for molecules that look like proteins or nucleic acids.
For general drug-like molecules, you want to use gaff2 atom types, since
they can deal with a much wider variety of chemical environments than can
Amber types.

So, run this again with "-at gaff2": this will avoid the DU problem, and
should allow you to proceed.

...good luck....dac

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Received on Sat Jan 23 2021 - 14:30:02 PST
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