AMBER Archive (2004)

Subject: Re: AMBER: How to neutralize system?

From: Marcin Krol (mykrol_at_cyf-kr.edu.pl)
Date: Wed Jun 09 2004 - 09:57:11 CDT

Just add one Na+ more and you will have almost zero charge, which I think
is fine.
Best
marcin

> Dear Amber Users:
>
> I have a system contains many hetero atoms and had managed producing
> parameters with antechamber. I found the unperturbed charge is not zero
> but -7.994000. After I added Na+ to the system by addions command,
> the charge is still not zero with the value of -0.994000. I'm not sure
> the charge would does matter to my MD process but I think it's safe to
> neutralize the system. Any helps would be very appreciated!
>
> Best!
>
> Liu
>
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