[AMBER] antechamber assigns DU as atom type for nitrogen

From: nguerin <nguerin.cs.duke.edu>
Date: Sat, 16 Jan 2021 22:47:04 -0500


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

parmchk2 -p $AMBERHOME/dat/leap/parm/parm94.dat -i dabrafenib.prepi -f
prepi -o dabrafenib.frcmod
Atom type of DU does not shown up in PARMCHK.DAT

I'm not sure what I should do. How can I get antechamber to recognize
N40 as a N2 atom type missing a hydrogen?

Thank you,

Nate Guerin
Duke University

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Received on Sat Jan 16 2021 - 20:00:02 PST
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