Re: [AMBER] binding free energy and pose analysis

From: case <>
Date: Fri, 27 Dec 2013 21:58:49 -0500

On Sat, Dec 28, 2013, Nitin Sharma wrote:
> I hope to find few more answers about molecular dynamics

A mailing list like this one is helpful in answering technical questions about
software like Amber. It is generally not a good place for very broad
questions like "what if my system isn't equilibrated?" or "what if I don't
know what pose my ligand should adopt?" These are very general questions that
don't have "answers": you need to be guided by your experience, and by reading
the literature. There is no one approach that is appropriate for all ligands
and receptors.

Furthermore, only you can answer the question of what you hope to achieve by
carrying out these simulations. The answer to this sort of question is
usually crucial in deciding what sort of calculation to undertake. For
example, do you want to get a rough estimate of binding in order to rank many
ligands in advance of experimental tests? Do you want to compare different
force fields or protocols to see which seem to work best for your sort of
problem? A you a novice who wants to see how free energy calclations work?
(etc.) All of these factors are relevant when planning a computational

Finally, concerning your specific questions: don't be afraid to experiment!
If you don't know whether to run your calculation "a bit more", try it and see
if the results are sensitive to such a change.

...good luck....dac

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Received on Fri Dec 27 2013 - 19:00:02 PST
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