AMBER Archive (2008)

Subject: Re: AMBER: AddIons approach

From: parul sharma (
Date: Fri Oct 10 2008 - 06:44:41 CDT

This is the leap.log, plea

Center of solvent box is: -28.161524, -18.774349, -9.387175
  Total vdw box size: 64.737 52.178 36.583 angstroms.
  Volume: 123570.855 A^3
  Total mass 55379.498 amu, Density 0.744 g/cc
  Added 3011 residues.
> addIons nmb Na 14 Cl 15
addIons: Argument #2 is type String must be of type: [unit]

    addIons unit ion1 #ion1 [ion2 #ion2]

        UNIT _unit_
        UNIT _ion1_
        NUMBER _#ion1_
        UNIT _ion2_
        NUMBER _#ion2_

Adds counterions in a shell around _unit_ using a Coulombic potential
on a grid. If _#ion1_ is 0, the _unit_ is neutralized (_ion1_ must be
opposite in charge to _unit_, and _ion2_ cannot be specified). Otherwise,
the specified numbers of _ion1_ [_ion2_] are added [in alternating order].
If solvent is present, it is ignored in the charge and steric calculations,
and if an ion has a steric conflict with a solvent molecule, the ion is
moved to the center of said molecule, and the latter is deleted. (To
avoid this behavior, either solvate _after_ addions, or use addIons2.)
Ions must be monoatomic. Note that the one-at-a-time procedure is not
guaranteed to globally minimize the electrostatic energy. When neutralizing
regular-backbone nucleic acids, the first cations will generally be added
between phosphates, leaving the final two ions to be placed somewhere around
the middle of the molecule.

On Fri, Oct 10, 2008 at 1:17 PM, Carlos Simmerling <> wrote:

> what does the leap.log file say?
> On Fri, Oct 10, 2008 at 7:13 AM, parul sharma <>
> wrote:
> > Dear Amber users,
> >
> > The problem i am facing is very strange, would be really thankful if you
> > could help me out with it. I tried to add ions to my peptides in water
> box,
> > but when i create the pdb after getting the 1000.rst file after sander
> > minimization, it doesn't show any ions in it.
> >
> > The leaprc looks like:
> >
> > source leaprc.ff96
> > loadAmberParams frcmod.WAT
> > solvateBox nmb TIP3PBOX 12
> > addIons nmb Na 14 Cl 15
> > saveamberparm nmb nmb.prmtop nmb.prmcrd
> > quit
> >
> > It gave me the crd and top files and i performed sander minimization, got
> > 1000.rst file, and it successfully crated the pdb too, but without ions.
> > Please help me.
> >
> > Kind Regards
> > Parul Sharma
> >
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to

The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)