Hi,
> and thanks for your quick answer. When I read the manual ifsc=2
> sounded ideally for my case, but as you explain it I would have to use
> ifsc=1. A good input option, in my case, would be to have a option
> similar to scmask that will zero the Lennard-Jones intermolecular
> interactions with the masked atoms. Now I have to prepare another
> prmtop file where I manually set the parameters to zero.
There is no need to manually set these parameters to zero (although it is
a valid way to do things I guess, similar to the dummy atom approach of
Amber9 and earlier). You can just build two systems, your solvated protein
complexed with benzene and your solvated protein alone. Then run these two
as the end states of your TI calculation and you are effectively
simulating the removal of benzene from the system (add restraints to that
and you have the setup to compute an absolute binding free energy)
Kind Regards,
Thomas
Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854
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Received on Wed Jan 13 2010 - 03:30:02 PST
