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 - 20:00:03 PDT
