Re: [AMBER] MM/PBSA calculation.

From: Jason Swails <>
Date: Mon, 23 Jun 2014 08:51:47 -0400

On Mon, 2014-06-23 at 15:39 +0530, Him Shweta wrote:
> Hi,
> I am using MM/PBSA for binding energy calculation for G-quaderuplex ligand
> system. In MM/ it is recomended to set born radii before making the
> topology file for ligand, receptor, complex and solvated complex.
> I just wanted to know which born radii i should use for G-quadruplex-ligand
> system.
> In the tutorial PBRadii is set to "mbondi2".

The radii you should use depend on the implicit solvent model you plan
on using.

See table 4.1 in the Amber 14 manual for more details relating to GB/SA.
While PB calculations are still sensitive to the definition of the
radii, I don't think they are _as_ sensitive to the starting radii of
the atoms as GB models are. That said, I don't know which radius set is
"recommended" for PB calculations (when using radiopt=0, of course --
radiopt=1 uses optimized radii instead of the ones in the prmtop file).

Of course if you do choose to compute PB electrostatics, you can try
different starting radii and see how much your answers change. ParmEd
can change the radii of your prmtop file directly without having to go
through tleap again.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Mon Jun 23 2014 - 06:00:04 PDT
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