If you are hoping for accurate numbers, that is a fairly complex question.
I would recommend reading up on biased molecular dynamics methods. I think
in the end you will have to try something like umbrella sampling. You
could get a rough idea using the adaptively biased molecular dynamics
module in AMBER, and then use that rough approximation to inform your
choice of windows for umbrella sampling. If you choose this route best to
read the ABMD section of the AMBER11 manual.
But honestly, if this is a protein trimer, you are probably unlikely to be
able to get an accurate answer using molecular dynamics unless you have
significant computational resources at hand.
~Aron
On Mon, Feb 20, 2012 at 6:06 AM, Ravleen, KAUR <
ravleenk.intern.bii.a-star.edu.sg> wrote:
> Hi,
>
> I have trajectory of a trimer(eg. ABC) but want to compute the binding
> energy of only a dimer(AB) in the presence/absence of the third monomer.
>
> How do I do that? Help is greatly appreciated!
>
> Regards,
> Ravleen
> Bioinformatics Institute, A*STAR (Singapore)
>
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Feb 20 2012 - 08:00:02 PST
