[AMBER] MMGBSA: interpretation of results

From: George Tzotzos <gtzotzos.me.com>
Date: Wed, 20 May 2015 14:09:19 +0200

I’ve run 3 consecutive MD simulations of 100ns each. A summary of delta-G total obtained by MMGBSA is given below.

1. homodimer. One of the chains treated as receptor the other as ligand. delta-G total -29kcal/mol
2. homodimer + 2 ligands (a & b). Used ante-mmpbsa.py to strip ligands (a & b) and generate topologies for chainA( to be treated as receptor) and chainB(to be treated as ligand). delta-G total -24kcal/mol
2. homodimer + 2 ligands (c & d). Repeated method used in 2. above. delta-G total -40 kcal/mol

Clarification: single trajectories were used.

Is such variation in delta-G total for binding of chainA to chainB to be expected? Is this due to perturbations upon ligand binding. Similar variation in delta-G was observed for binding of ligands to the dimer and the same ligands to the monomer (DIFFERENT MD runs)

My objective is to determine whether the ligands stabilise or not dimer formation. Is the approach described above suitable for the purpose?

Thank you in advance for any comments/suggestions



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Received on Wed May 20 2015 - 05:30:02 PDT
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