Hello Amber,
I'm using "ntr=1, restraintmask=" to run targeted MD. In the tutorial it's wrote that "the molecule is ’fitted’ implicitly by applying positional restraints to atoms specified in restraintmask". I wander in Amber if the these atoms (in restraintmask) of the initial structure is aligned to the corresponding atoms in the reference structure before running targeted MD? This is important for me. Thank you!
Best,
Yao Li
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Received on Thu Jul 19 2018 - 20:00:01 PDT
