Re: [AMBER] randomly place counterions

From: <>
Date: Wed, 2 Mar 2011 17:07:02 +0100

Hi Thomas,

I have to admit that my experiences with leap and counter ions are probably a
bit outdated, but from what I remember there were different reasons why
haven't tried leap yet:

1) leap places the ions according to the electrostatic potential, and thus
you always have a protein within a swarm of ions but the rest of the solvent
is just...solvent.
2) at least older versions of leap (don't know if this is still the case for
the current one) sometimes just stopped placing ions even when the number of
ions that I wanted to add wasn't reached yet. Thus, you wouldn't be
guaranteed get a neutralized system.
3) one of the reasons that placing the ions according to elstat potential was
the thing to do is probably due to much lower simulation times - if you only
have 100ps for equilibration, you probably want to start with ions close to
distinguished points where the electrostatic potential absolutely requires a
ion to be there - otherwise you'd probably never have it go there during the
short simulation time. Im not sure if this is still an issue these days -
maybe someone out there has an opinion on that. I would guess that a mixed
procedure - populating regions where the elstat pot absolutely demands it +
some randomly distributing other ions in the simulation box is what I really

Does anybody have experience with these issues? Or am I a bit overconcerned
and it doesn't really matter how and if at all one places counterions (after
all the "PME aether" does take care of much of it...)


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: []
Gesendet: Mittwoch, 2. März 2011 13:42
An: AMBER Mailing List
Betreff: Re: [AMBER] randomly place counterions


> 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,


Dr. Thomas Steinbrecher
formerly at the
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Wed Mar 02 2011 - 08:30:04 PST
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