Dear AMBER users,
I am trying to reproduce the change in enthalpy of binding of
protein-ligand complex using MMPBSA . In the paper, Authors' used amber12
version and cavity_surften, cavity_offset were set as 0.005420, -1.008
respectively.
Whereas, I am using amber22 version, in this case, default values of
cavity_surften, cavity_offset are 0.0378, -0.5692 respectively. When my
calculations were done using the default (cavity_surften, cavity_offset
parameters), the result matched closely enough with the paper. But,
when I explicitly
mentioned the cavity_surften, and cavity_offset parameters (based on the
paper) in "mmpbsa.in" file, I am getting positive enthalpy change of
binding !! Could you kindly give suggestions regarding this?
Your suggestions would be highly appreciated.
Thanks and regards
Kankana Bhattacharjee
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Received on Fri Aug 25 2023 - 13:00:02 PDT
