Dear AMBER
I am calculating the QM/MM-GBSA binding energy. The QM region covers the ligand and few residues of the protein.
The energy terms is some way confused. One recent email post here discusses the energy components.
I have two questions:
Firstly, why QM-MM van der waals interactions are included in VDWALLS classically? what the reason behind it? I read many papers showed semi-empirical methods could estimate van dar waals interaction in a good agreement with ab initio methods.
The second question is that I calculated the energies of the ligand, receptor and the complex using QM/MM method. I used the conventional equation of calculating the binding energy:
dG=(BOND+ANGLE+DIHED+VDWAALS+EEL+EGB+1-4 VDW+1-4 EEL+AM1ESCF+ESURF)complex -(BOND+ANGLE+DIHED+VDWAALS+EEL+EGB+1-4 VDW+1-4 EEL+AM1ESCF+ESURF)ligand-(BOND+ANGLE+DIHED+VDWAALS+EEL+EGB+1-4 VDW+1-4 EEL+AM1ESCF+ESURF)receptor
Sure, in case of ligand, BOND+ANGLE+DIHED+VDWAALS will be zero.
I am just afraid to miss something. is that all or should I pay attention to something else?
Thanks
Eliac
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Received on Sat Jan 01 2011 - 20:30:01 PST
