the AMBER implementation of tmd allows a single reference
coordinate, so you would probably want to use the complex with A
as initial structure and complex with B as the reference.
All that the tmd controls is the RMSD of current structure to the
reference. It seems possible that you could set up the type of
simulation that you describe, but it isn't something
obvious and you need to spend some time thinking
about how to make the change between complex with A and B.
tmd might not be the best approach. I think this is more
complex that the typical applications have been, you might want
to look in the literature and see what has been done.
----- Original Message -----
From: "hj zou" <hjzou.iris3.simm.ac.cn>
To: <amber.scripps.edu>
Sent: Wednesday, February 18, 2004 9:58 PM
Subject: AMBER: tmd question
> dear amber users，
> Now I wanna perform a tmd simulation using amber.But I'm not sure
whether it can work or not.
> I have two proteins,protein A and protein B, which form complex.The
initial structure is protein A with a ligand C complexed with unbound
protein B.The target structure is protein B with the ligand C complexed with
unbound protein A.
> Can anyone tell me whether TMD can experience such a conformational
change and provide insight into the process of conformational change?If not
,is there any other method to tackle this problem?
> Any suggestions are appreciated.
>
> best regards
> 2004-02-19
>
>
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Received on Thu Feb 19 2004 - 16:53:00 PST
