Re: [AMBER] antechamber QM calculation/qmcharge error

From: Rui Chen <>
Date: Thu, 21 Nov 2019 09:48:38 -0700

Dear David,

Please find attached the input pdb file for the ligand. The charge is -1, I
used -nc flag to specify the charge of the system. Is that correct? By the
way, the ligand already has hydrogens before using antechamber.

antechamber -i 6058_rep0_pose1.pdb -fi pdb -nc -1 -o 6058_rep0_pose1.mol2
-fo mol2 -c bcc

I check the sqm.out file, the calculation is completed.

Best regards,


On Thu, Nov 21, 2019 at 6:34 AM David A Case <> wrote:

> On Wed, Nov 20, 2019, Rui Chen wrote:
> >
> >QMMM: System specified with odd number of electrons ( 141)
> >QMMM: but odd spin ( 1). You most likely have the charge of
> >QMMM: QM region (qmcharge) set incorrectly. Correct error and re-run
> >calculation.
> This shows that something is wrong with your input files; are all the
> hydrogens present? Have you specified the charge of the molecule (if it
> is not zero)?
> >Instead of using bcc charge method, I used gas charge method,
> Gasteiger charges are not likely to be very accurate. Plus, if you
> don't have the proper net charge on the molecule, any charge method will
> be dramatically wrong. Bottom line: you need to fix the problem
> identified above before proceeding.
> ...good luck...dac
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Received on Thu Nov 21 2019 - 09:00:02 PST
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