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

From: Chetna Tyagi <cheta231.gmail.com>
Date: Thu, 24 May 2018 16:01:19 +0200

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
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Received on Thu May 24 2018 - 07:30:02 PDT
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