AMBER Archive (2007)

Subject: Re: AMBER: PME and counter ions

From: Pablo Englebienne (pablo.englebienne_at_mcgill.ca)
Date: Wed Dec 19 2007 - 13:05:30 CST


addIons mol Na+ 250

Why not using "addIons mol Na+ 0"? That would ensure that the system has
a neutral charge... Did you get any warning out of LEaP?

-- 
Pablo Englebienne, PhD Student, Moitessier research group
Department of Chemistry, McGill University
801 Sherbrooke Street West
Otto Maass bldg, room 206
H3A 2K6 Montréal, Québec, Canada
Tel (514) 398-5501    Fax (514) 398-2382

"Progress is made by lazy men looking for easier ways to do things." - Robert A. Heinlein

Lars Skjærven wrote: > Sorry for being imprecise.. > > Yes, water was added after adding the ions as recommended in the amber > manual. The number of counter ions added corresponds to the charge of > the protein so it is neutralized, ofcourse. :-) > > charge mol > addIons mol Na+ 250 > solvateBox mol TIP3PBOX 8 > > Lars > > On Dec 18, 2007 7:36 PM, Bill Ross <ross_at_cgl.ucsf.edu> wrote: > >>> We are simulating a protein of ~7500 residues using PME with pmemd. It >>> is quite negatively charged, so we added ~250 counter ions (Na+) with >>> the Leap (function addIons). The protein is really unstable, which is >>> not what we expected. >>> >> Did you add water too? >> >> Bill >> >> ----------------------------------------------------------------------- >> The AMBER Mail Reflector >> To post, send mail to amber_at_scripps.edu >> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >> >> > ----------------------------------------------------------------------- > The AMBER Mail Reflector > To post, send mail to amber_at_scripps.edu > To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu >

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