Re: [AMBER] Help in ligand preparation_antechamber

From: David A Case <>
Date: Tue, 11 Jan 2022 10:20:00 -0500

On Mon, Jan 10, 2022, Arooma Maryam wrote:

>I am working on a ligand that is covalently bound to FAD cofactor. . *Both
> PO4s meioties of FAD together have -2 whereas the drug part has -1 (please
>see par.pdb). *Overall charge on this FAD bound drug is -1.

Do you not mean the drug part has charge of +1 (formally at the N1
position)? That would lead to a net charge of -1 for the whole ligand.

Your "par.pdb" file has duplicate atom names: atoms 17 and 18 are both
named "N1", atoms 21 and 22 are both named "C2", etc. Antechamber will
rename duplicate atoms, but that makes the atom names in the mol2 file
differ from those in the input PDB file, and makes it very hard to do any
debugging. Start with an input PDB file where the atom names are unique.

> To prepare this compound, i used this command
>*antechamber -i par.pdb -fi pdb -o lig.am1bcc.mol2 -fo mol2 -c bcc -s 2
>-nc -1*
>*but the output lig.am1bcc.mol2 shows 0 charge and two PO4 meioties have
>also changed. *

??? The sum of the charges in the mol2 file is -1, just as you requested for
with the "-nc -1" flag. I'm not sure why you think it "shows 0 charge".

For a di-phosphate system like this one, I'd recommend turning off geometry
optimzation at the bcc step: add -ek "qm_theory='AM1' maxcyc=0" to your
antechamber run. This will dramatically speed up the sqm calculation, and
should lead to somewhat better charges.

Bottom line, though: your ligand may actually be correctly parameterized,
but the atom name problem should be fixed before going forward.
Try a minimization on just the ligand itself to see what it does to the

....good luck....dac

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Received on Tue Jan 11 2022 - 07:30:03 PST
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