Enhanced sampling of domain motion and gsafold

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

• Next message: Ben Lowe: "Calculating electrostatic force from NAMD trajectory"
• Previous message: Dhiraj Srivastava: "Fwd: enhanced sampling of domain motion, GSAfold"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

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

• Next message: Ben Lowe: "Calculating electrostatic force from NAMD trajectory"
• Previous message: Dhiraj Srivastava: "Fwd: enhanced sampling of domain motion, GSAfold"
• Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]

This archive was generated by hypermail 2.1.6 : Sun Dec 31 2017 - 23:21:25 CST