Re: [AMBER] binding free energy- error calculation doubt

From: Elvis Martis <>
Date: Wed, 22 Feb 2017 12:21:12 +0000

The value of uncertainty aka standard deviation (If I am right here) is larger than your mean value which I unacceptable.
This means that there is large uncertainty in your calculations.
My best guess will be to look whether you trajectories have achieved equilibrium.

    Best Regards

Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A  Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12

-----Original Message-----
From: Mary Varughese []
Sent: Wednesday, February 22, 2017 4:30 PM
To:; AMBER Mailing List <>
Subject: Re: [AMBER] binding free energy- error calculation doubt


If I write the uncertainty as is it, will be like (-6.45+_10.39) the uncertainty greater than value. Is it ok?
Is uncertainty in T of delta TS available.?
In some papers I see they include uncertainty (of delta G) also. but its very small value; less that one.

I asked about uncertainty term in hbond distance: its another doubt. Is anyone familiar with it. Its a review question I got. I don't understand how should I comment it.

Thanking you

mary varughese

On Tue, Feb 21, 2017 at 6:49 PM, David Case <> wrote:

> On Tue, Feb 21, 2017, Mary Varughese wrote:
> >
> > Below is the result i got for a receptor ligand system in mmpbsa
> > binding energy calculation. enthalpy and entropy parts. Could any
> > one help me, how to calculate the uncertainty part in delta G from
> > this result?
> You have uncertainties in PBTOT and TSTOT, so combine those using the
> usual error propagation rules to estimate the uncertatinty in the sum.
> >
> > Also how could i include the uncertainty or error in hbond distance
> > (receptor ligand hbond) calculation obtained using ptraj on a
> > complex trajectory. Could i include error if i calculate hbond
> > distance on a single representative structure in vmd?
> I don't understand what you want here: you could use cpptraj to
> compute the ditribution of H-bond distances in your snapshots. That
> is not related in any direct way to uncertainties in energies,
> however.
> ....dac
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