Dear AMBER Developers
I am trying to re-evaluate FEP calculation of converting Methanol with a lone pair to Methane as done in "Richard, W. D.; Peter, A. K., Advancing beyond the atom-centered model in additive and nonadditive molecular mechanics. Journal of Computational Chemistry 1997, 18, (13), 1632-1646"
For free energy calculation, the author studied conversion of methanol to methane as following:
Methanol(lp)---> Methane
CH3-O(EP)-H ---> CH3-H(Y)-X
X is a dummy atom of hydrogen with zero charge and Y is an EP with zero charge, is that right?
If yes, let me ask one more question, according to extra_pts.f file, the 1-4 nonbonds are getting from the bond list (the one not involving hydrogens). Here, Y (which is EP) is attached to H atom, so I couldn't understand how in this case 1-4 non-bonds are calculated?
I NEED your HELP, PLEASE
Any kind of help would be appreciated.
Thanks in advance
Flak
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Received on Sat Aug 28 2010 - 19:00:04 PDT
