[Molecular-modelling] A question about implementing MM-PBSA method by CHARMM

Zhang Xin zhangxin at scbit.org
Sun Jul 31 21:43:21 EST 2005


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



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