AMBER Archive (2007)

Subject: AMBER: mm_pbsa individual contributions of residues

From: AYTUG TUNCEL (ATUNCEL_at_ku.edu.tr)
Date: Mon Mar 05 2007 - 17:12:54 CST

Dear all,

Which one is a better method for estimating the important residues (by mm_pbsa) in the interaction process. Applying the decomposition of free energies into individual contributions or applying the decomposition of free energies by pair interaction energies? What I want to say is that, for ex. residue x in chain A and residue y in chain B has a 96 % occupancy over the trajectory according to the hbond analysis. And when I apply the decomp_pair method for this pair I obtain -2.28 kcal indicating a favorable interaction between these residues. But when I decompose the free energies of these resiues into individual contributions I obtain -1.07 for residue x and +0.86 for residue y. This result indicates a disfavorable contribution from residue y and a little favorable contribution from residue x to the total binding free energy. So according to result 1 can we conclude that the residues x and y are important (in a favorable fashion) for the interaction and according to result 2!
  c!
an we conclude that residue y is disfavoring the interaction? Are these results contradicting? Can somebody clarify the situation? Thanks in advance.

Aytug Tuncel vidual contributions or applying the decomposition of free energies by pair interaction energies? What I want to say is that, for ex. residue x in chain A and residue y in chain B has a 96 % occupancy over the trajectory according to the hbond analysis. And when I apply the decomp_pair method for this pair I obtain -2.28 kcal indicating a favorable interaction between these residues. But when I decompose the free energies of these resiues into individual contributions I obtain -1.07 for residue x and +0.86 for residue y. This result indicates a disfavorable contribution from residue y and a little favorable contribution from residue x to the total binding free energy. So according to result 1 can we conclude that the residues x and y are important (in a favorable fashion) for the interaction and according to res

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