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
>>
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