AW: free energy of binding

From: Norman Geist (
Date: Thu Jul 07 2011 - 05:35:07 CDT

I don't know the procedure for NAMD but it can be done with QM/MM calculations using CPMD very fine.

Mit freundlichen Grüßen

Norman Geist.

-----Ursprüngliche Nachricht-----
Von: [] Im Auftrag von Francesco Pietra
Gesendet: Donnerstag, 7. Juli 2011 11:53
Betreff: namd-l: free energy of binding

How could free energy of binding of a small-molecule ligand to a
protein receptor be calculated from namd md trajectories?
Is there a validated specific procedure for namd, or should a
literature method be imitated? For example Åqvist's method:

Åqvist, J., Medina, C., and Samuelsson, J. E. (1994) A new
method for predicting binding affinity in computer-aided drug design.
Protein Eng. 7, 385–391.

thanks for sharing experience on this hot topic

francesco pietra

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