Hi
A new question arises then: can I apply the restraint only to the
benze state? As I specify restraints on the benzene molecule in the
DISANG file it will not make sense to apply this same restraints to a
system without benzene.
/ Samuel
2010/1/13 <steinbrt.rci.rutgers.edu>:
> 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 - 04:30:05 PST
