From: Corum, Katharine W <katharine-corum.uiowa.edu>
Date: Wed, 5 Oct 2016 15:05:19 +0000
Hi Everyone,
I want to perform QM/MM calculations on a protein that has an organic molecule covalently bonded to one of the residues, using Amber16. So far I have only modeled ligands that are not covalently bonded. I used Antechamber and tleap to prep my ligands and residues for the structures with the ligand not covalently bound. I looked at the archive and found some past emails and tutorials. However most of these date pretty far back. Some of these tutorials are for a single metal bonded to the protein but I assumed I could follow the same steps for my organic molecule. Before I start diving in I want to check to see if there are any tutorials more relevant to my situation that I did not find. Or if I can use the same tutorials with Amber16 since a couple of these links date back to Amber8 and I am sure there have been a lot of changes since then.
Thank you for any advice! The links are below to tutorials that I have read that I think could be helpful to me.
Amber Workshop - Tutorial A1<http://ambermd.org/tutorials/advanced/tutorial1_adv/>
ambermd.org
(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple ...
Amber Tutorials - A1 - Setting up an Advanced System ...<http://ambermd.org/tutorials/advanced/tutorial1/section1.htm>
ambermd.org
There are several options for charge fitting in AMBER. This includes the original RESP implementation, Antechamber and R.E.D. For a standalone ligand one would ...
