[AMBER] understanding results

From: Carlos Romero <carlos.rom.74he.gmail.com>
Date: Wed, 17 May 2017 13:46:28 -0500

Dear all.
I have one question regarding to MD results interpretation.

I want to know how changes the response of one protein when it is in
diferent pH.

My know about Molecular Dynamics is that resulting trajectories are the
possibles conformations of a molecule after being applied some energy, many
of them are not possible because wrong conformations, but some of them are
probably right. Among these structures, is one with the lowest potential
energy, which is the most probably in nature.

I run MD on my protein, in two ways, the fist one is exactly as the
crystallographic structure, and the other one, with protonated residues. I
took both structures, with lowest potential energy and dock to its natural
ligand, The first one, had a relatively high score when docked to the known
binding site, the second, never docked to known binding site.

Is it a reasonable way to interpret that conformation change of protonated
state, changes enough that molecule lose affinity to its natural ligand? or
are necessary another techniques for reinforce interpretion of MD

Thanks in advance.

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Received on Wed May 17 2017 - 12:00:03 PDT
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