Hi,
from what you send me it seems like you are removing a complete ligand to
get the total binding free energy. That is a pretty advanced type of
simulation and not easy to get to reasonably converged results. You
probably have to introduce restraints at some point before your ligand
diffuses away, plus getting a smooth vdW curve even for small ligands can
be tricky. This is quite a complicated research project, so be sure to
experiment a lot and follow other peoples work on the topic (B. Roux and
M. Shirts groups come to mind among others)
> I am also running few more lambda values for vdw decoupling in order to
get better convergence.
be prepared to make that many more and longer simulations...
Sorry, but I couldn't see your attachment, as it's docx, but feel free to
resend the curves in an open format,
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Tue Oct 05 2010 - 04:00:03 PDT
