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

From: Gustavo Seabra <>
Date: Sat, 9 May 2015 17:04:03 -0300

Hi William,

If I can offer one advice it is that, before you do QM/MM MD on this system, make sure you can run a regular MD with it first. Usually, the protocol I like to follow is to first minimize/heat/equilibrate system with regular MD, and only then turn on QM. Then, you may want to run a short equilibration on the QM/MM hamiltonian first before you can start collecting data.

BTW, notice that just because it has “QM” in the name it doesn’t mean the hamiltonian will necessarily be better than a well balanced force field, unless you are dealing with then making/breaking of chemical bonds, or some special charge transfer effects.

Good luck!
Gustavo Seabra

> Em 09/05/2015, à(s) 16:35, William Martin <> escreveu:
> Hello,
> 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.). I'm not looking
> for a step-by-step walkthrough (though if one exists that would be great!),
> but a few guidelines would be super helpful. If it is important, a .pdb
> exists for the protein with the ligand of interest in place, but future
> studies will involve docking new molecules.
> Thanks in advance!
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Received on Sat May 09 2015 - 13:30:03 PDT
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