On Mon, Jan 19, 2015, Hadeer ELHabashy wrote:
>
> I am trying to apply AMBER Advanced Tutorial 22
> <http://ambermd.org/tutorials/advanced/tutorial22/section1.htm> of the
> Accelerated molecular dynamics on my target protein to detect some
> conformational change. And I found the second section of Generating and
> Relaxing the Initial Structure very impressive and complete. Can I apply
> the same protocol "with some minor changes to suite my protein" on my
> structure and then run normal MD instead of AMD ?!!
Sure: the tutorials are just examples of calculations. As long as you
understand what is going on, you are encouraged to try new things. Don't be
afraid to experiment: no two simulations are the same, and trying out differnt
options is a good way to gain practical experience.
....dac
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Received on Sun Jan 18 2015 - 17:30:03 PST
