Dear AMBER community,
I am trying to construct a thermodynamic cycle where I subtract
MMPBSA-determined gas phase free energy differences from TI calculated free
energy differences to get solvation free energy differences. I looked at
the AMBER 20 manual, and it says that setting gti_add_sc to 3 should cause
all ELE and VDW to be scaled, which should imply VDW and ELE free energy
differences are calculated when running TI. Of course bonded interactions
would have to be subtracted from MMPBSA energies for this
thermodynamic cycle, but just as far as VDW and ELE charges are concerned,
from what I understand it seems that the gti_add_sc=3 option should cause
comparable numbers to be obtained by both TI and MMPBSA in the context of a
thermodynamic cycle. Could someone please confirm for me that this is
correct?
Thanks in advance,
Holly Freedman
Cheatham Group
University of Utah
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Received on Thu Jun 03 2021 - 11:30:02 PDT
