Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber

From: Matias Machado <>
Date: Tue, 01 Sep 2020 11:38:41 -0300 (UYT)

well... you will get an energy value indeed (cpptraj can't distinguish between FG or CG)... however the meaning of that energy will likely differ...

In CG the potential energy surfaces is always a free energy surface, that's because you are condensing several degrees of freedom into single beads or topologies (e.g. side chain rotations), and hence part of the entropy is captured by the parameters ("the potential energy": the enthalpy)... the "captured amount" depends on the CG model and how it was derived (i.e. by fitting to free energy of to other property)... in case of SIRAH, models are fit to structural properties, then the absolute energy values is likely to "mean nothing", but the relative ones do... Indeed the self-consistence within the force field (i.e. hydrophobicity and hydrophilicity) is given by the relative interaction among all particles, however the reference energy isn't a particular well known thermodynamic quantity (e.g. hydration free energy)

To get a feeling on what I'm saying, You can check this paper, in which authors use SIRAH 1.0 to calculate Protein-Protein Binding Free Energies:

Interesting, SIRAH 1.0 outperforms FoldX in most of those benchmarks... I expect SIRAH 2.0 to do much better... :-)



----- Mensaje original -----
De: "Charo del Genio" <>
Para: "Matias Machado" <>
CC: "AMBER Mailing List" <>
Enviados: Sábado, 29 de Agosto 2020 10:52:09
Asunto: Re: [AMBER] Questions (and a small bug report) about SIRAH in Amber

On 28/08/2020 17:57, Matias Machado wrote:
> Just for the record of this thread...
> I've just uploaded a new release version of SIRAH for AMBER [version: x2.2_20-08] to our web [], including the bugfix for the LJoff.fcrmod issue.
> It was tested to correctly work on cmake and legacy builds of AMBER Tools 19 and 20.
> Enjoy it!
> Matías

Thank you very much, that's great!

By the way, do you happen to have some suggestion on how to do energy analysis on a coarse-grained trajectory? I would normally use "energy" and "lie" from cpptraj, but I am not sure they would give
sensible results after CG. What is your suggestion?



Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
Applied Mathematics Research Centre (AMRC)
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Received on Tue Sep 01 2020 - 08:00:02 PDT
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