AMBER Archive (2004)

Subject: AMBER: Binding free energy from separate/single trajectory

From: yuann (yuann_at_bioinfo.ndhu.edu.tw)
Date: Sun Dec 12 2004 - 23:01:17 CST

Dear all,
  Currently I compared two ways (from separate/single trajectory)
for estimating the binding free energy (via MM-GBSA/nmode (AMBER7)).
Results from separate trajectories were much better than those from single
trajectory (compared with experiment result). Is it reasonble or
problematic in my simulation system? (geometry checks of the trajectories,
like RMSd, were done and seemd to be fine during 5ns.)

  Another question, for estimating the binding free energy between
a receptor(R, DNA here) and two indentical ligands(L), we should get it by
estimating delta_delta_G = delta_G2 - delta_G1 ?
R + L --> RL (delta_G1)
RL + L --> LRL (delta_G2)

Thank you very much!

Sincerely,
yuann.

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