[gmx-users] Ligand Internal energy

[Mark Abraham]

On 6/09/2012 12:15 PM, Marcelo Depolo wrote:
> I am not from the area but I believe that a quantum approach is needed for
> proper validation of protein-ligand complex.
> Use Gromacs in order to lead you to the best frame (or pose), but calculate
> the energies in a quantum perspective.

Well that would be better if feasible. The basic limitation of MM force 
fields is that the charges are fixed at parameterization time, and do 
not change in response to their environment. Proteins bind ligands in 
part because they offer a more suitable environment for the ligand, 
which means each will polarize the other. So the usual approach to 
charge in the MM methodology is fundamentally limited here.

Mark