AMBER Archive (2003)

Subject: Domain/Helix movement/MD

From: Jianhui Wu (wujih_at_BRI.NRC.CA)
Date: Fri Jan 31 2003 - 10:35:18 CST

Dear All,

I am seeking some adivce on simulating the large domain (or Helix)
movement on ligand binding. I tried the MD simulations with GB model for a
few ns but the large conformational change indicated by biochemical data
still can not be detected by the simulations. Except for the explicit
water simulations and the high temperature MD, are there other better
strategies?

If you successfully detected the large conformational change by MD, would
you point me to some references and share your experience?

Regards,

Jian Hui