Dear AMBER users,
I hope this email finds you well. I am currently using the thermodynamic integration module implemented in AMBER 20 to calculate the absolute binding energy of a cation to a protein pocket. To achieve this, I am attempting to let one cation inside the pocket vanish while simultaneously letting the one in the bulk appear. I am using a harmonic potential to restrain the pocket-located ion and a softcore potential to smooth the van der Waals energy.
However, I have encountered a problem. When I checked the snapshots of the lambda=0.240452 run, I observed that the two cations have strangely collided together. The cation in the bulk moved inside the pocket, and they are now only 1.1 Å apart. I am concerned that when lambda reaches 1, the ion that should have been in the bulk may become stuck and unable to diffuse into the bulk, which is incorrect.
I would greatly appreciate your help in determining if this phenomenon is normal in TI simulations, or if I have made some errors. Here are the TI parameters I am currently using:
icfe=1
clambda=0.240452
timask1=":913.Na+"
timask2=":914.Na+"
ifsc=1
scmask1=":913.Na+"
scmask2=":914.Na+"
gti_chg_keep=0
ntf=1
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Received on Thu Mar 16 2023 - 09:30:02 PDT
