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

From: Charo del Genio <>
Date: Tue, 1 Sep 2020 16:06:44 +0100

On 01/09/2020 15:38, Matias Machado wrote:
> 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... :-)
> Best,
> Matías

Hi Matias,
        thank you very much again, your explanation is very clear.



Dr. Charo I. del Genio
Senior Lecturer in Statistical Physics
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Received on Tue Sep 01 2020 - 08:30:02 PDT
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