[AMBER] binding free energy and pose analysis

From: Nitin Sharma <sharmanitin.nus.edu.sg>
Date: Sat, 28 Dec 2013 01:52:50 +0800

Respected sir,

I hope to find few more answers about molecular dynamics

I am following the amber tutorial to calculate binding free energy. With respect to production phase it is mentioned that "It is essential, for good results, that our system still be exploring equilibrium phase space during the production phase" . On my study I am using molecular dynamics (MD ) to analyze different ligand against same protein but I for some ligands I have reached a decent equilibration after 30ns but for some RMSD is still increasing. Can I use these trajectories for the analysis or I should run a bit more for each protein-ligand system so that each one of them reaches equilibrium phase?

What would be better option for selecting the possible pose for the ligand? The final pose after MD or pose with lowest energy or continuing the MD with simulated annealing for about 1ns and accepting the resultant pose?

If I use simulated annealing to predict the pose how can I deal with binding free energy calculation? Shall I use the trajectory resulted from MD to calculate binding free energy or the simulated annealing trajectory for that purpose? Can I even combine MD and simulated annealing trajectory and use that for binding free energy calculation?

Thanks in advance

Nitin Sharma
Department of Pharmacy,Faculty of Science,National University of Singapore,block S7, Level 2, Singapore : sharmanitin.nus.edu.sg<mailto:sharmanitin@nus.edu.sg> ; http://www.linkedin.com/in/imsharmanitin

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Received on Fri Dec 27 2013 - 10:00:03 PST
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