Re: [AMBER] MMGBSA: estimating "effective energy" convergence

From: Casalini Tommaso <>
Date: Wed, 2 Nov 2016 13:44:17 +0000


I am dealing with the same problem.
Right now, I am trying to compute the energetic contribution of the binding using and using the flag -eo energyout, which gives you the energy values for each considered frame for complex, receptor and ligand. You can check the convergence over simulation time.
I hope this can help.
All the best,

Tommaso Casalini, PhD
Post Doctoral Fellow
ETH Zurich
Institute for Chemical- and Bioengineering
Morbidelli Group, HCI F137
Vladimir-Prelog-Weg 1
8093 Zurich, Switzerland
Phone: +41 (0)44 632 61 83

-----Original Message-----
From: George Tzotzos []
Sent: Mittwoch, 2. November 2016 14:39
To: AMBER Mailing List <>
Subject: [AMBER] MMGBSA: estimating "effective energy" convergence

I’m dealing with a homodimer and have calculated the “effective energy” of binding of the two subunits using MMGBSA.

The calculation was done from as single trajectory MD simulation.

In order to check whether the “effective energy” of binding has converged, I would like to extract the time-series of the sums of gas-phase energies and solvation free energies as computed for the trajectory snapshots of the unbound subunitA, subunitB, and the complex subunitA – subunitB.

I guess, I can do this by parsing the temporary files obtained (e.g. _MMPBSA_complex_gb.mdout) that contain the energy components. My question is if there is a better way of doing what I described above.

Thanks in advance for any suggestions

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Received on Wed Nov 02 2016 - 07:00:04 PDT
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