RE: add ions

From: Blake Charlebois (
Date: Mon Aug 08 2005 - 09:34:41 CDT


You can use the SODIUM program ( to place ions in electrostatic
potential minima. If your protein is positively charged and you need to add
negative counterions, you will want to reverse the charges on all protein
atoms in the PDB input file (see Tcl code at the bottom of this email),
allow it to place sodium ions, and manually change these to chlorine ions.

The protein-electrolyte system is complex, and exhibits chaos. It therefore
gives different results even when the simulation protocol is the same. It is
often difficult to know whether a change in simulation protocol affects
results in a meaningful way. I have found that it is easy to spend (waste)
too much time worrying about ions. Does anyone have an opinion on this?

Ions placed by SODIUM should be equilibrated. You might need to extensively
equilibrate randomly-placed counterions. Placing the ions based on the
Poisson-Boltzmann equation might reduce or eliminate the need for ion
equilibration, but this might not be worth the extra effort. Pfeiffer,
Fushman, and Cowburn (reference below) compute a rather long required
equilibration time (2 ns for 27 mM NaCl?) based on Hubbard (I doubt whether
Hubbard's theory is entirely applicable to a protein-electrolyte system).
Can anyone confirm their calculation?

A lot of the precedent for including ions in MD systems seems to be from
simulations of nucleic acids.

Blake Charlebois
References addressing ion equilibration:

J.B. Hubbard, "Non-equilibrium theories of electrolyte solutions," in The
physics and chemistry of aqueous ionic solutions, 1st ed., vol. 205, M.-.
Bellissent-Funel and G.W. Neilson Eds. Dordrecht ; Boston; Norwell, MA,
U.S.A.: D. Reidel Pub. Co.; Kluwer Academic Publishers, 1987, pp. 95-128.

S. Pfeiffer, D. Fushman and D. Cowburn, "Impact of Cl- and Na+ ions on
simulated structure and dynamics of beta ARK1 PH domain," Proteins, vol. 35,
pp. 206-217, MAY 1. 1999.
Other references addressing ions:

G.T. Ibragimova and R.C. Wade, "Importance of explicit salt ions for protein
stability in molecular dynamics simulation," Biophys.J., vol. 74, pp.
2906-2911, JUN. 1998.

B.N. Dominy, D. Perl, F.X. Schmid and C.L. Brooks, "The effects of ionic
strength on protein stability: The cold shock protein family," J.Mol.Biol.,
vol. 319, pp. 541-554, MAY 31. 2002.
Reference suggesting ions are not very important:

H. Fan and A.E. Mark, "Relative stability of protein structures determined
by Xray crystallography or NMR spectroscopy: A molecular dynamics simulation
study," Proteins, vol. 53, pp. 111-120, OCT 1. 2003.
Tcl commands for making a PDB file for SODIUM (you should check that this
gives you the right output):

        set fname yourfile

        mol load psf $fname.psf pdb $fname.pdb

        set ev [atomselect top all]
        set indices [$ev get index]

        foreach ind $indices {
                set at [atomselect top "index $ind"]
                $at set beta [$at get charge]
                #$at set occupancy 0
                $at delete

        # delete and reload due to paranoia
        mol delete top
        mol load psf $fname.psf pdb $fname.pdb

        set ev [atomselect top all]
        $ev writepdb "$fname.chargesinB.pdb"

        foreach ind $indices {
               set at [atomselect top "index $ind"]
               $at set beta [expr -[$at get charge]]
               #$at set occupancy 0
               $at delete

        set ev [atomselect top all]
        $ev writepdb "$fname.revchargesinB.pdb"
        mol delete top

-----Original Message-----
From: [] On Behalf
Of Mahalakshmi Sahasranaman
Sent: August 8, 2005 8:42 AM
Subject: namd-l: add ions

Dear Users,

I want to do a energy minimization and then a MD
simulation for trypsin-BPTI complex. I need to add 15
Cl- ions in positions of largest electrostatic
potential and fix these counterions during all
simulations. Is it possible ?

If not, placing Cl- ions randomly for trypsin-BPTI
complex, would it give the same results instead of
having Cl- in the positions of largest electrostatic
potential ?

Thank you very much for your help.


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