Re: [AMBER] MM-PBSA and handling of ions

From: Bill Miller III <>
Date: Mon, 31 Jan 2011 17:51:57 -0500

The perl script will keep the atoms that you tell it to keep in the
extract_coords.mmpbsa input file in the .MAKECRD section when you specify
the START and STOP atom numbers for the ligand and receptor. Typically, all
ions are removed during MM-PBSA calculations. This is probably the best
method since the implicit solvent models used by MM-PBSA (PB and GB) are not
parameterized very well for explicit ions. You can specify the salt
concentration within the GB and PB sections as a substitute for explicit
ions. This will take into account a specified salt concentration during the
calculation without including explicit ions. The only time one would want to
keep explicit ions is if the ions were critical for binding. In these cases,
including the explicit ions must be done with care and the user should know
all the implications of how this will affect the calculation.

I hope that helps!


On Mon, Jan 31, 2011 at 5:12 PM, Jagur Lambix <> wrote:

> Hello AMBER users,
> I am calculating the free energy of binding of my protein+ligand system.
> In my MD generated trajectory there inclusion of WAT molecules and Cl-
> ions.
> I was just following the AMBER advanced tutorial-3, to get an idea about
> the
> calculation and to apply in my system.
> However, in the tutorial there is NO addition of any ions.
> The perl script (extract_coords.mmpbsa) does the removal of WATER from the
> trajectory and saves the new coordinates for protein, ligand and the
> complexes.
> However, my question is that, does the script removes ions (Cl-) too ?
> If NOT, do I need to remove the ions for the calculation. Please let me
> know how
> to handle the ions during these type of calculations.
> Need your suggestions in this regard.
> Thanks and best wishes
> Jagur
> _______________________________________________
> AMBER mailing list

Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Mon Jan 31 2011 - 15:00:07 PST
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