Dear amber users,
I want to calculate the PMF as a function of the distance between the center
of mass (CM) of the CA atoms of two proteins as I detach them. My intended
protocol is:
(1) single steered MD simulation to generate initial conformations at
different CM distances.
(2) umbrella sampling simulations at different CM distances.
However, I am confused as to how to define the restraint between the two
CM's. Can I use something like this in the restrain file?
*restraint = "distance( com(:1-178.CA) com(:179-748.CA) )"*
Best regards,
Jose M. Borreguero
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Received on Sun Oct 10 2010 - 08:00:03 PDT
