enhanced sampling of domain motion, GSAfold

From: Dhiraj Srivastava (dhirajks_at_gmail.com)
Date: Sat Jul 01 2017 - 23:49:00 CDT

Hi all
       I want to simulate my protein to sample different domain
conformations that I can use for docking. I want to keep the two domain
rigid and the two linkers flexible as I am expecting the domain motion of
almost 80 A or 180 degree rotation around the hinge.
 I read that GSA might be helpful in this situation and its implemented in
NAMD but I am not finding a good manual or tutorial about it.
does anyone have any suggestion or manual/tutorial on GSAfold in NAMD?


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