Re: [AMBER] Atom type of NO does not shown up in PARMCHK.DAT

From: David A Case <>
Date: Tue, 28 Sep 2021 16:09:58 -0400

On Tue, Sep 28, 2021, Reza Esmaeeli wrote:
>I am trying to parametrize a nucleotide analog with a NO2 functional
>group on the base. After running antechamber and getting the mol2 file, I
>get the following error from parmchk2:
>Atom type of NO does not shown up in PARMCHK.DAT

Can you say what command-line arguments you gave to antechamber and to
parmchk2? Providing the input pdb file (or similar) that you gave to
antechamber would also help.

Atom types in capital letters (like NO) are supposed to be Amber atom types,
but PARMCHK.DAT indeed knows nothing about NO. There are no NO2 functional
groups in proteins or nucleic acids, so that is hardly suprising. But I don't
know how you got a NO type assigned in the first place.

If you came up with this "by hand", then you will need to prepare a frcmod
file by hand as well. Use GAFF atom types (as a test) for your model. You
will probably see atom type "no" (lower case) for your nitrogen. Copy
parameters that involve it to the frcmod file, changing "no" to "NO" and
adapting the atoms types of the atoms it is bonded to as needed.

...good luck...dac

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Received on Tue Sep 28 2021 - 13:30:02 PDT
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