Re: [AMBER] binding energy calculations

From: kirtana S <>
Date: Mon, 9 Apr 2012 16:25:06 -0400

Will this give meaningful results if I use the trajectory obtained from the
explicit water simulations by removing water and using nobox to obtain my
new trajectory.
And use a vacuum topology file of the polymer by itself .
Can I obtain the solvation free energy using MMPBSA.

On Sat, Apr 7, 2012 at 3:09 PM, Jason Swails <> wrote:

> On Sat, Apr 7, 2012 at 2:57 PM, kirtana S <> wrote:
> > Sorry for not using the right terminology . I have used explicit solvent
> > simulations.
> > I want to calculate the change in solvation free energy of polymer in
> > presence of ions.
> >
> > Is this only for implicit solvent models.
> >
> The MM/GBSA methodology is pretty much limited to implicit solvent models.
> The problem with using explicit solvent models with these types of
> calculations is that convergence is nearly impossible. For
> moderately-sized periodic boxes, the total energy is dominated by
> solvent-solvent interactions, which means that any protein-solvent or
> protein-protein interactions will be drowned out completely for a handful
> of snapshots. The only way you can get meaningful statistics is if you use
> so many snapshots that the noise contributed by solvent-solvent
> interactions is averaged out.
> Keep in mind that noise will drop off as 1/sqrt(N) where N is the number of
> frames in your averaging -- therefore, for large noise (which this is), it
> will require a _large_ number of snapshots to get your desired
> interactions.
> Implicit solvent, on the other hand, models equilibrium solvation
> properties -- i.e., it should average over the solvent degrees of freedom,
> completely eliminating the noise caused by explicit solvent.
> Note that implicit solvent models can incorporate generalized ionic effects
> via the introduction of a debye screening parameter (for GB) and the
> Boltzmann part of the PB equation which can be truncated after the first
> order term in the salt concentration (linear PB) or carried out to the sinh
> term (non-linear PB). The manual for explains how to set salt
> concentrations (or ionic strengths) for MM/GBSA and MM/PBSA.
> Of course this will not capture the effect of structurally important ions
> -- this is a much more difficult problem.
> HTH,
> Jason
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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Received on Mon Apr 09 2012 - 13:30:02 PDT
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