Hi,
> 1. I have tried to use free energy calculation but failed.
> 2. Is the procedure I listed in my last email reasonable ? (list as
> follows)
> 3. one protein + (10 ~ 20 ligand) will swell and have 2 to 3 times size of
> its orginal shape. That is known from
> the experimental work => we want to knwo if the simulation can show
> this phenomena too.
1. With no more information, we cannot really help there. Did you have a
look at the free energy tutorials on the amber homepage and could
reproduce the data from there? What exactly 'failed' when you tried it on
your system?
2. The procedure you list is not wrong per se, however I do not understand
why you build your system in two steps. Why not add 18 ligands to the
protein right away, solvate and simulate?
3. To me this sounds more like a denaturation experiment than ligand
binding. Be sure to check that the time scale on which the original
experiment is supposed to happen is within range of your simulations.
Protein unfolding can take many orders of magnitude longer than it is
possible to simulate.
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jan 06 2010 - 06:00:07 PST
