Hi dear all.
I am working in protein interactions en presence of ions. I make
simulations according to AMBER tutorials.
The procedure I follow is the next:
When I have a complex, I separate receptor and ligand with a text editor.
I add ions, solvate, do minimizations, heating and Dynamic simulations
according to Tutorials.
When the dynamics finish, normally I get a PDB file by ampbdb utility from
both molecules, receptor and ligands, and I make a docking using Hex 6.3.
It is the way I thought I could observe a conformational change in both
molecules and see if in presence of ions have the same behavior.
But I was looking in literature if this procedure was correct and I found
that the way of analyse the results is diferent.
My question is: could anybody help me in suggets literature for what means
a dinamyc molecular simulation?, and how can I interpret results?
I searched in the internet but it is a lot of information and I really
don't understand so much.
I appreciate your comments.
Regards
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Received on Thu Feb 11 2016 - 09:30:05 PST
