Re: [AMBER] Self Inconsistency within antechamber for NAD and NAP cofactors (expects different bond orders in different routines)

From: David A Case via AMBER <>
Date: Mon, 5 Jun 2023 16:50:59 -0400

On Mon, Jun 05, 2023, Christopher Corbo via AMBER wrote:
>I have noticed a potential issue in amber16 & 20 for systems which contain
>NAD and NAP (3 letter pdb codes) cofactors.
>The issue arises because when I pass the mol2 into antechamber for bcc
>charges, ...

Can you say what you mean by "the mol2"? Where did this come from? Does it
have all the hydrogens present?

I don't think we can understand what is going on (and hence try to help)
without seeing the input you gave to antechamber. Please include the
command line flags you used, as well.


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Received on Mon Jun 05 2023 - 14:00:03 PDT
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