Enhanced sampling of domain motion and gsafold

From: dhirajks_at_gmail.com
Date: Mon Jul 03 2017 - 19:18:38 CDT

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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?

thanks
Dhiraj
Sent from my iPhone

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