Re: [AMBER] randomly place counterions

From: Hugh Heldenbrand <>
Date: Wed, 02 Mar 2011 09:16:29 -0600

On 03/02/2011 08:59 AM, Kevin Hauser wrote:
> Hi,
> 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.
I am no AMBER master, but I think that this method would lead to ion
concentrations that are not quite right in a constant pressure
simulation. xleap's solvent boxes place water molecules on a grid whose
spacing results in a density is less than what the system's equilibrium
density will be after a few picoseconds of simulation (and if you were
to run at constant volume you would end up with "vacuum pockets" due to
not having enough water molecules to fill the box at equilibrium).
Basically, the volume that xleap prints out will not be volume of your
actual simulation.

In the past what I have done is run a short simulation of pure water at
constant pressure/temperature to determine what the density of my water
model is. Then, I use the number of water molecules xleap places (also
printed out by leap after solvating the system) and that density in the
calculation of how many ions are need to reach a particular 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
I second the recommendation of Professor Cheatham's updated ion parameters.
> HTH,
> kevin
> 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

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Received on Wed Mar 02 2011 - 07:30:04 PST
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