hi,
I'm trying to using MM-PBSA method to estimate changes in binding free
energies of protein-protein complexes as a result of mutating one or
more residues. So far as I know, most people prefer using AMBER to
compute the molecular mechanic terms and using DELPHI, with PARSE radii
and Cornnel charges, to compute electrostatic contribution to solvation
free energy. When I using CHARMM to do the same job, the results becomes
quite different from those published ones (e.g. Irina Massova & Peter
A. Kollman, J. AM. CHEM. SOC., 121(36), 8133-43). I tried to adjust
protein dielectric constant, but the result is still not encouraging.
Dos this come from the parameter differnece between AMBER and CHARMM? I
appreciate if any one can share his/her experience in this aspect.
p.s. It is the first time I post to bionet groups. please tell me if
there is anything improper.
best regards,
--
Cean
