Re: [AMBER] binding free energy and pose analysis

From: Nitin Sharma <>
Date: Sat, 28 Dec 2013 18:42:59 +0800

Respected sir,

Can you tell me if it will correct approach to combine MD and simulated annealing trajectories?

Thanks and regards,
Nitin sharma

-----Original Message-----
From: case []
Sent: Saturday, December 28, 2013 10:59 AM
To: AMBER Mailing List
Subject: Re: [AMBER] binding free energy and pose analysis

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 strategy.

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 Sat Dec 28 2013 - 03:00:02 PST
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