Hi,
I want to use the AMBER-Gaussian QM/MM approach to simulate the first solvation shell around a nucleoside..I want to start from an MD structure but i'm worried about the charge conflict issue..For different forcefield AMBER uses different scheme although at the end all may be near because of antechamber, but if i start MD with a definite charge value, from for example DFT like the ff03 FF, if i perform QM/MM the charge of the QM region will be much different as at this case antechamber is not there to balance the charge...or, do i need to choose a certain charge scheme such as MK to derive and to use in the context of the QM-MM interaction...Also, can i choose a DFT functional for the QM region such as B3lyp although my simulation has been already prepared with HF according to the ff99SB scheme.....
Marawan
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Received on Wed Sep 26 2012 - 00:00:02 PDT
