Hi
Thanks. I will more or less follow the work of Roux (which also are
cited in the manual) except for the way of simulation and calculation
dG.
/ Samuel
2010/1/13 <steinbrt.rci.rutgers.edu>:
> 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.
>
> Yes, restraints can differ between systems (or be applied for only one
> system), for precisely that reason. You can set dvdl_norest=1 if you want
> sander to automatically subtract the restraint contributions from dvdl,
> where they should not be counted.
>
> A note of caution: This feature hasnt been used very much so far and it
> assumes that V0 is the state with restraints and V1 the state without. It
> *should* work the other way round as well, but you are very much
> beta-testing here, look at your outputs with care.
>
> Also, you will have to do several additional calculations about adding the
> restraints, removing the charges first, reappearing the molecule in water
> and apply an analytical correction for the restraints. You probably know
> all that from the literature, I wanted just to point out that the result
> from this one TI calculation will have no connection to experiment on its
> own.
>
> 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 - 05:00:04 PST
