AMBER Archive (2004)

Subject: Re: AMBER: How to neutralize system?

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Wed Jun 09 2004 - 09:58:37 CDT

Hi,
-7.994000 is pretty close -8. If you add 8 Na+, your system will have a
net charge of 0.006, thought not zero, but quite small and should be OK.

Guanglei

scopio wrote:

> 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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