Re: [AMBER] antechamber problem with negatively charged nitrogen

From: David A Case <>
Date: Mon, 21 Sep 2020 08:20:29 -0400

On Mon, Sep 21, 2020, Giorgos Lambrinidis wrote:
>Thank you for your reply. Regarding our knowledge Nitrogen 3 must have 2
>single bonds in order to carry the negative charge. O1 and O2 must have
>double bond with carbon 11 and carbon9 respecively.
>The structure generated has single bond between Carbon9 and Oxygen1
>suggesting negative charge to the oxygen1 instead of nitrogen3. If this is
>correct i have to check it again. The question is why antechamber changed
>the ionization from nitrogen to oxygen? I shall check the literature and i
>shall come back later.

Just remember three things: first, antechamber is making suggestions, and
they may not always be correct; some things have to be assigned by hand.
Second, the charges come largely from the quantum calculations, so are
independent of what antechamber thinks the valencies are; (you might want
to use RESP charges to get complete independence). Third, Amber
makes no use of bond orders, so there may be occasional problems there that
don't get noticed.

You can check the extent to which the structure and vibrational
frequencies predicted by GAFF2 match those from quantum mechanics. Might
be interesting to see what the open force field initiative's "parsley"
force field gives for this molecule.

...good luck....dac

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Received on Mon Sep 21 2020 - 05:30:03 PDT
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