Re: [AMBER] MM/PBSA calculation.

From: Him Shweta <>
Date: Mon, 23 Jun 2014 22:51:17 +0530

Thanks Jason for your inputs, I saw the table in Amber14 manual.

**********Input file that i am using for calculation is as

   endframe=100, interval=1, keep_files=0, strip_mask=:WAT, Na+,
  exdi=80, indi=1.0,
  inp=1, cavity_surften=0.00542, cavity_offset=0.92,
  fillratio=4, scale=2.0, prbrad=1.4, radiopt=0,

*******For entropy calculation using NMode, the input file is:-************

   endframe=100, keep_files=0, strip_mask=:WAT, Na+,

   nmstartframe=1, nmendframe=100,
   nminterval=1, maxcyc=10000, drms=0.001,

So, using the above input file i calculated the binding energy and entropy.
I am using ff99 force filed for running simulation in NPT ensemble using
TIP3P water model.
When i calculated the binding energy and entropy without setting default
radii to mbondi2 before saving the topology files for ligand, receptor and

The result that i got is Delta G=-21.46 kcal.mol and TdeltaS= -20.32

And when i calculated the binding energy and entropy after setting the
PBRadii to mbondi2.
The result that i got is Delta G=-22.02 kcal.mol and TdeltaS= -13.44

Here in both the calculation value of entropy has changed much and value of
delta H is more or less within the error limit.

I need your comments and suggestions on this.
Thanks a lot in advance.

On Mon, Jun 23, 2014 at 6:21 PM, Jason Swails <>

> 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.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Jun 23 2014 - 10:30:02 PDT
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