AMBER Archive (2004)

Subject: Re: AMBER: add charge error message: Number of electrons is odd

From: David A. Case (case_at_scripps.edu)
Date: Fri Oct 22 2004 - 16:12:00 CDT

On Fri, Oct 22, 2004, berry1027 Eric wrote:

> Dear all, When I run the following command " antechamber -i btn.pdb -fi pdb
> -o btn.prepin -fo prepi -cc bcc", it happen the error message:
> Total number of electrons:129; net charge:0
> Number of electrons id odd: 129
> Please check the total charge and your -nc flag.

Antechamber is only parameterized for "closed shell" molecules, which by
definition have an even number of electrons. The neutral version of the pdb
file you used has an odd number of electrons: perhaps the molecule should be
charged. If so, use the "-nc" (Net charge) flag to tell antechamber what
overall charge to use.

...good luck...dac

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