AMBER Archive (2008)

Subject: Re: AMBER: Amber : neutralizing without adding ions

From: Lars SkjŠrven (
Date: Mon Jan 14 2008 - 09:41:55 CST

Hi Jani,
Are you using PME? If so, this has been discussed earlier. I would
therefore recommend reading this thread:

and/or search for "PME and counter ions" like this in google and
you'll get the whole thread: amber "PME and counter ions"

Good luck. :-)

Lars SkjŠrven

On Jan 14, 2008 12:43 PM, jani sahil <> wrote:
> Hello
> I am new to amber and i want to simulate an acid protease
> for which i need to neutralize the structure. I need to neutralize without
> adding any ions
> is their any way to do this
> Thanks in advance
> Regards
> Jani Vinod

mvh Lars SkjŠrven
Institutt for Biomedisin
Universitetet i Bergen
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