AMBER Archive (2008)

Subject: Re: AMBER: reg.building ions

From: David A. Case (
Date: Fri Dec 12 2008 - 06:42:28 CST

On Fri, Dec 12, 2008, balaji nagarajan wrote:
> Please check the total charge and your -nc flag

If the charge of your system is not zero (the default), you have to set it
with the -nc flag, e.g. "-nc 3" for a +3 ion.

> For atom[1]:Co, the best APS is not zero, exit

As I wrote earlier, antechamber is not going to be able to handle molecules
with metal atoms.


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