Re: [AMBER] Plotting phi-psi plots with free energy scale

From: Carlos Simmerling <>
Date: Thu, 24 May 2018 10:13:33 -0400

I don't think residue decomposition would be helpful for you. Most often
the free energy as a function of phi/psi is calculated from populations
sampled during the simulation. This assumes that the populations are well
sampled and in a Boltzmann weighted distribution. If sampling is slow,
other methods such as umbrella sampling can be used.

There are many examples and a description of methods in the ff99SB force
field paper:

Comparison of multiple Amber force fields and development of improved
protein backbone parameters
Hornak, V., Abel, R., Okur, A., Strockbine, B., Roitberg, A. and
Simmerling, C.
Proteins: Structure, Function and Bioinformatics , 2006 , 3 (3), 712-725
DOI: 10.1002/prot.21123
PMCID: PMC4805110

On Thu, May 24, 2018 at 10:01 AM, Chetna Tyagi <> wrote:

> Dear all,
> Is there any easy way to calculate free energy along the simulation
> coordinate for each residue as post-process?
> Methods like TI seem to be really long.
> I performed a MMGBSA based residue-wise energy decomposition analysis on
> one peptide. (This is not a complex and so I am not interested in binding
> free energy).
> The output is a big file with various energy values for each residue in
> every frame.
> If I want to make a phi-psi plot with one of these energy terms as the
> third column, which energy term should I select?
> And how should I extract this information?
> Or is there any other easy way to *plot phi-psi plots with free energy used
> as scale* to show energetically stable conformations?
> Any advice is appreciated.
> --
> Best wishes
> Chetna
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Received on Thu May 24 2018 - 07:30:02 PDT
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