AMBER Archive (2008)

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

From: Lars Skjærven (lars.skjarven_at_biomed.uib.no)
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:
http://structbio.vanderbilt.edu/archives/amber-archive/2007/4731.php

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

Good luck. :-)

Lars Skjærven

On Jan 14, 2008 12:43 PM, jani sahil <genomejani_at_gmail.com> 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 Skjærven
Institutt for Biomedisin
Universitetet i Bergen
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu