[AMBER] Should I Perform Docking Before Simulation To Find Realistic Binding Score With MMPBSA ?

From: Erdem Yeler via AMBER <amber.ambermd.org>
Date: Sun, 26 Jun 2022 12:48:20 +0300

In one of the papers, the authors experimentally demonstrated the
interaction between the ligand and the protein. The MMPBSA did not find any
binding when I simulated the same protein-ligand for 10 ns. Autodock, on
the other hand, says there is an interaction, even if it is weak (-4.6
kcal/mol). Normally, I would create a complex with the docking process
before doing the simulations and then start the simulation, and I had
always found results very close to the experimental results until now. This
time I just used tleap's combine command while creating the complex. Could
this be the reason why I can't find the ligand-protein interaction? So is
it really necessary to dock and start the simulation with the docked
complex before molecular dynamics or should I extend my simulation?
Thank you
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Received on Thu Aug 04 2022 - 13:33:20 PDT
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