Hi,
We are learning TIcomputation using pmemd. One thing we noticed is that,
we mutated ligand0 (50 atoms) to ligand1(52 atoms) in solution with 30 common atoms (# of softcore atoms are 20 and 22, respectively, certainly). The computed DeltaG was -20 kcal/mol.
When we reduced # of common atoms to a few atoms, the computation gave DeltaG of -4 kcal/mol.
I think this is not because of sampling issue but about how DV/DL is counted. (in the manual, it said only non-bonded interactions of soft core atoms contributes to DV/DL, not bonded interaction).
Considering Delta G is a state function, at the first look, DeltaG should be the same even # of common atoms is reduced.
My guess is that this "effect" will be cancelled out in the thermodynamic cycle.
along this thinking, it seems that, suppose we want to reproduce sander's DeltaG using pmemd, we need to make the right choice of common atoms. (I am still thinking about this!)
comments are welcome and appreciated.
thanks.
Ying-chieh
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Received on Mon Nov 24 2014 - 08:30:03 PST
