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

From: Christopher Corbo via AMBER <>
Date: Mon, 5 Jun 2023 23:23:38 -0400

Hi Dr. Case,

Thank you for the speedy reply.

  antechamber -fi mol2 -fo mol2 -c bcc -j 1 -at sybyl -s 2 -pf y -i
${system}.cof.processed.mol2 -o ${system}.cof.am1bcc.mol2

Is the command run to generate bcc charges. I realize the -j flag set to 1
is pointless as it ultimately gets overridden for bcc calculations. This is
the step changing the bond order of the nicotinamide ring for bonds
(N6-C21) and (N6-C16). (Sorry, the files I am attaching end up with
different atom names than those in the original email I sent).

   antechamber -i ../001.lig-prep/${system}.cof.am1bcc.mol2 -fi mol2 -o
${system}.cof.ante.prep -fo prepi

Is the command which throws a Fatal error for the reassigned bond types.
(Open valence on C16). However if I use the bond orders which are present
in ${system}.cof.processed.mol2 the step runs successfully.

I am including an example for each of the cofactors, although the issue is
essentially the same for both.

Thank you again for the help, it is appreciated!

On Mon, Jun 5, 2023 at 4:50 PM David A Case <> wrote:

> 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.
> ...thx...dac

Christopher Corbo
Ph.D. Student
Department of Biochemistry and Structural Biology
Member of the Rizzo Lab
Stony Brook University

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Received on Mon Jun 05 2023 - 20:30:02 PDT
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