Re: [AMBER] QM/MM Protein-Ligand interaction w/cofactor

From: William Martin <>
Date: Sun, 10 May 2015 01:27:30 -0400

Fortunately those are questions I already have answered, as I've been doing
work in Gaussian using ONIOM on the same protein. I'll work on getting a
regular MD run going first, thanks!

On Sat, May 9, 2015 at 10:43 PM, David A Case <>

> On Sat, May 09, 2015, William Martin wrote:
> >
> > New user of AMBER, poked through a few tutorials. Looking to do QM/MM MD
> > on a protein/ligand complex with a cofactor. Various places give
> > conflicting information on how to handle all of it (leave the ligand in,
> > take it out, leave the cofactor in, take it out, etc.).
> Gustavo's advice is good here. The question of whether the ligand or
> cofactor
> should be a part of your simulation has nothing to do with QM or not: it
> depends on what you want to learn from the simulation. When the time
> comes to
> go from MM to QM/MM, you really just have to decide what level of QM to
> use,
> and which atoms should be in the QM region. These are difficult questions,
> and there are no universal answers or cookbook solutions.
> ....dac
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Received on Sat May 09 2015 - 22:30:02 PDT
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