[AMBER] Binding energy of ligand with homology model

From: Morrow,John Kenneth <JKMorrow.mdanderson.org>
Date: Thu, 21 Dec 2017 19:45:31 +0000

Hello, I have a small molecule inhibitor of a protein-protein interaction, and AMBER simulations of the complex shows the ligand can undergo significant rotations and (almost 180 among 1 axis) and different conformers. The ligand is small and really only has 3 major functional groups<https://pubchem.ncbi.nlm.nih.gov/compound/1286902>. It is worth mentioning that this binding pocket is not complete, so the starting structure was built from a homology model.

I would like to have some binding energy calculations of the ligand in these different conformations. I found this post discussing the different methods:
http://archive.ambermd.org/201204/0277.html But as this post is over 5 years old, I would like to ask the community if there are any newer recommendations/thoughts. Simulation time is not a concern, but ease of use is, as I am a relatively novice AMBER user.

Thank you,


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Received on Thu Dec 21 2017 - 12:00:02 PST
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