Re: [AMBER] Charge error in Antechamber.

From: Bruno Falcone <>
Date: Fri, 24 Feb 2017 14:04:54 -0300

Hi Vatsal,

You're probably missing a proton somewhere. You could also obtain an
estimate of the total charge if you assign gasteiger charges to your
molecule and then add up all the atomic charges. For that use the -c gas
keyword in antechamber. You don't need to assign -nc in this case.

If you're still having problems I'm happy to check your structure if
you're allowed to share it.



On 24/02/17 13:50, Vatsal Purohit wrote:
> Dear all,
> I am trying to use antechamber on a mol2 file and am getting the following
> error:
> Total number of electrons: 547; net charge: -5
> INFO: Number of electrons is odd: 547
> Please check the total charge (-nc flag) and spin multiplicity (-m
> flag)
> Running: /apps/amber/amber14/bin/sqm -O -i -o sqm.out
> Error: cannot run "/apps/amber/amber14/bin/sqm -O -i -o sqm.out" of
> bcc() in charge.c properly, exit
> Looking at the molecule and counting the number of charged atoms, I
> calculate the charge to be -5 and am hence confused about why I am getting
> this error.
> Could it be perhaps, that my estimate of charge is off due to partial
> charges in the molecule? Is there a software / program I could use to
> determine the charge of the molecule before entering it in AMBER?
> Kindly, advise.
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Received on Fri Feb 24 2017 - 09:30:02 PST
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