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

From: Mary Varughese <>
Date: Wed, 22 Feb 2017 16:30:02 +0530


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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Received on Wed Feb 22 2017 - 03:30:02 PST
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