[AMBER] MM-PBSA and handling of ions

From: Jagur Lambix <jagurlambix.yahoo.com>
Date: Mon, 31 Jan 2011 14:12:06 -0800 (PST)

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

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Received on Mon Jan 31 2011 - 14:30:05 PST
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