From: Dong Luo (us917_at_yahoo.com)
Date: Thu Jul 07 2011 - 10:50:07 CDT
AmberTools has utilities to calculate free energy of binding from a single MD trajectories that simulated with Amber force field. NAMD supports Amber force field.
I recently did a test with this. It works though I am not sure of the quality of the results because it's the first time for me to calculate the binding free energy.
Briefly the steps are:
1. Convert pdb file to Amber friendly format according to AmberTools' manual. The online tool: http://glycam.ccrc.uga.edu/ccrc/GlycamLITE/Protein/uploadIndex.jsp?option=ff99 can help with it.
2. Using AmberTools' tleap to create parameter and coordinates input files for MD. Again check with the manual.
3. Edit NAMD configuration file to use the Amber force field. Check NAMD's guide.
4. Run the simulation.
5. Calculate the free energy of binding following corresponding steps in the Amber tutorial:
From: Francesco Pietra <chiendarret_at_gmail.com>
To: NAMD <namd-l_at_ks.uiuc.edu>
Sent: Thursday, July 7, 2011 5:52 AM
Subject: 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
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