Re: [AMBER] randomly place counterions

From: <>
Date: Wed, 2 Mar 2011 07:42:17 -0500 (EST)


> 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 - 05:00:04 PST
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