Re: [AMBER] randomly place counterions

From: <>
Date: Wed, 2 Mar 2011 17:25:48 +0100

Hi Kevin,

thanks a lot for your input...randomizeions is certainly worth a try (didn't
know this command), and thanks also for the hint to the ion parameters!

Maybe I miss something - but wouldn't it be just possible to calculate the
number of ions from the number of solvating water molecules? Yes - then one
would have to run leap twice as well, but this is certainly the least
cost-intensive part of the whole procedure :-)

All the best,

Mit freundlichen Grüßen / Kind regards,
Dr. Thomas Fox

Boehringer Ingelheim Pharma GmbH & Co. KG
Lead Identification and Optimization Sup
Tel.: +49 (7351) 54-7585
Fax: +49 (7351) 83-7585

Boehringer Ingelheim Pharma GmbH & Co. KG, Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR A 22206; Komplementär Boehringer Ingelheim
Deutschland GmbH; Geschäftsführung: Dr. Engelbert Günster (Vorsitzender),
Ralf Gorniak, Mark Hagmann, Michael Klein, Dr. Martin Wanning; Vorsitzender
des Aufsichtsrates: Prof. Dr. Dr. Andreas Barner; Sitz: Ingelheim am Rhein;
Registergericht Mainz: HR B 23260

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-----Ursprüngliche Nachricht-----
Von: Kevin Hauser []
Gesendet: Mittwoch, 2. März 2011 15:59
An: AMBER Mailing List
Betreff: Re: [AMBER] randomly place counterions


You ought to be able to have leap determine and add counterions
automatically by using the following cmd,

addions foo Na+ 0

if your solute is net negative, and it is sodium that you desire. Logical
modification if other ion or solute is net positive can be made,

addions foo Cl- 0

Note that the "0" in the cmd commands leap to add enough ions to counter
solute charge, which I assume is your desire.

See the previous emails in this thread to randomize your ions - ptraj *
randomizeions*. Calculating your concentration ought to be
semi-straightforward if you're using a solvent box - leap prints the volume
of the box after solvating the system. Thus, you have to run leap twice,
first to solvate the system and determine your volume, and then a second
time to add ions, if you wish to add ions in addition to counterions, and
are matching molarity Not molality.. I'm not 100% on your question, so I
added the blurb about adding ions in addition to counterions.

Amber masters, please correct me if i'm wrong on having to run leap twice to
determine concentration.

As a final note, Professor Cheatham's lab has developed ion parameters
specific for solvent type, e.g. TIP3P. You'd have to load these parameters
in your leap script. The parameters for TIP3P would be named "frcmod.ions*jc
*_tip3p" and ought to be in your $amberhome/dat/leap/parm directory. This is
just my humble thought though - I would recommend reading the article,
"Determination of Alkali and Halide monovalent ion parameters for use in
explicitly solvated biomolecular simulations" *2008, *JPCB

On Wed, Mar 2, 2011 at 7:56 AM, Hugh Heldenbrand <> wrote:

> On 03/02/2011 06:42 AM, wrote:
> > Hi,
> >
> >> does anybody have a script or program that takes a solvated protein
> >> structure
> >> (as pdb file) and then randomly replaces water molecules by counterions
> ?
> >> Preferentially, it would lead to a neutralized system and would take a
> >> concentration as input.
> > xleap in amber does something *like* this, but it places ions at
> > electrostatically reasonable positions instead of randomly (which might
> be
> > preferable...). Check the addions command.
> >
> > source leaprc.ff10
> > foo = loadpdb<name.pdb>
> > addions foo Na+ 5 Cl- 3
> > savepdb foo<newname.pdb>
> >
> > It does read and write pdb files, if they contain only protein and water.
> >
> > Kind Regards,
> >
> > Thomas
> >
> > Dr. Thomas Steinbrecher
> > formerly at the
> > BioMaps Institute
> > Rutgers University
> > 610 Taylor Rd.
> > Piscataway, NJ 08854
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> If you want random ion positions after placing them with xleap, you can
> use ptraj to do this. See the "randomizeions" command on page 120 of
> the AmberTools 1.4 manual.
> -Hugh Heldenbrand
> Grad Student, University of Minnesota
> _______________________________________________
> AMBER mailing list

-- - -
Kevin Eduard Hauser
National Science Foundation,
LSAMP Bridge to the Doctorate Fellow
The Department of Chemistry
Stony Brook University
Stony Brook, New York 11794
Phone: (561) 635.1848
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Received on Wed Mar 02 2011 - 08:30:07 PST
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