Re: [AMBER] free energy calculation

From: David Case <>
Date: Thu, 26 Sep 2019 20:04:16 +0000

On Thu, Sep 26, 2019, Sadaf Rani wrote:

>I am writing this email again in hope to get a reply on a problem which I
>am facing regarding free energy calculation. From mailing list earlier I
>asked about free energy calculation tutorial and I could not get reply.

It is next to impossible to get any Amber developer(or users) to look
at older versions of tutorials and bring them up to date. So, don't
treat tutorials as a cookie-cutter that should be followed blindly.
Rather, try to understand what is going on, compare the scripts that are
there to what is in the Reference Manual, and see if you can create
your own inputs that advance your understanding of how to proceed.

You might want to look at the FEW tutorial; it, however, is it bit

[I recognize that there is great interest among some in the Amber
community in running TI calculations of ligand binding events. It would
be most helpful if people with such interests could either update the T4
lysozyme example (which is 10 years old, updated 5 years ago), or
provide a more recent example.]

...good luck....dac

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Received on Thu Sep 26 2019 - 13:30:01 PDT
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