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

From: David Case <>
Date: Tue, 21 Feb 2017 08:19:54 -0500

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.


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Received on Tue Feb 21 2017 - 05:30:09 PST
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