Tommaso,
Grateful for the hint.
Best wishes
George
> On 2 Nov 2016, at 15:44, Casalini Tommaso <tommaso.casalini.chem.ethz.ch> wrote:
>
> Hi,
>
> I am dealing with the same problem.
> Right now, I am trying to compute the energetic contribution of the binding using MMPSA.py 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,
> T.
>
>
> Tommaso Casalini, PhD
> Post Doctoral Fellow
> ETH Zurich
> Institute for Chemical- and Bioengineering
> Morbidelli Group, HCI F137
> Vladimir-Prelog-Weg 1
> 8093 Zurich, Switzerland
> tommaso.casalini.chem.ethz.ch
> Phone: +41 (0)44 632 61 83
>
>
>
> -----Original Message-----
> From: George Tzotzos [mailto:gtzotzos.me.com]
> Sent: Mittwoch, 2. November 2016 14:39
> To: AMBER Mailing List <amber.ambermd.org>
> 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
>
> George
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Received on Wed Nov 02 2016 - 08:00:02 PDT
