OK, thanks for this final confirmation !
Best wishes,
Marek
Dne Thu, 26 Jan 2012 18:18:03 +0100 <steinbrt.rci.rutgers.edu> napsal/-a:
> Hi,
>
>> So I don't understand fully your notice "The analytical correction does
>> not have any connection to this, but is a separate step (without MD
>> simulation) you probably have to do.".
>> Probably you had on your mind just k*T*ln(Fr), k*T*ln(Ft*C0) corrections
>> or there is some way how to estimate also dGsite_r and dGsite_t
>> contributions without special TI run ?
>> Maybe usually these contributions are neglected as especially in cases
>> of
>> strongly interacting ligands these corrections are sufficiently small ?
>
> ok, what I said may have been imprecise, the analytical correction is a
> separate step, but the cost of switching on the restraints while the
> ligand fully interacts is yet another third leg of your cycle that indeed
> needs a numerical result from MD simulations. I dont think it is a
> contribution that can typically be neglected, unless you set very weak
> restraints.
>
> Thomas
>
> Dr. Thomas Steinbrecher
> formerly at the
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
>
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Received on Thu Jan 26 2012 - 10:00:03 PST
