Dear AMBER community,
I'm trying to use amber20 thermodynamic integration to get absolute binding free energy for a protein-ligand complex.
I've set input parameters as
"
icfe = 1, ifsc = 1, clambda = LAMBDA, scalpha = 0.5, scbeta = 12.0,
logdvdl = 1,
ifmbar=1, mbar_states=11, mbar_lambda=0.00, 0.10, 0.20, 0.30, 0.40, 0.50, 0.60, 0.70, 0.80, 0.90, 1.00,
timask1 = ':NAP', timask2 = '',
scmask1 = ':NAP', scmask2 = '',
"
in TI section as to get absolute free energy according to amber20 manual.
However, when I'm checking the mdout files from each lambda window, I noticed that the DV/DL value out put for each 1000 steps in TI region1 & TI region2 are identical to each other throughout the whole simulation.
I'm wodering whether this output is right or not? If not, which part of the input file should I revise?
Sincerely,
Songyan Xia
PhD candidate
School of Medicine
The Chinese University of Hong Kong, Shenzhen
China
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Received on Thu Mar 23 2023 - 03:00:02 PDT
