[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,

John

The information contained in this e-mail message may be privileged, confidential, and/or protected from disclosure. This e-mail message may contain protected health information (PHI); dissemination of PHI should comply with applicable federal and state laws. If you are not the intended recipient, or an authorized representative of the intended recipient, any further review, disclosure, use, dissemination, distribution, or copying of this message or any attachment (or the information contained therein) is strictly prohibited. If you think that you have received this e-mail message in error, please notify the sender by return e-mail and delete all references to it and its contents from your systems.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 21 2017 - 12:00:02 PST
Custom Search