Hi Thomas,
thanks for your answer !
Just the last question regarding your notice below.
It is clear to me that the r, t restraint corrections k*T*ln(Fr),
k*T*ln(Ft*C0) (as formulated in Roux articles) to compensate
restraining (decrease in degrees of freedom) of the non-interactig
(decoupled) ligand in binding site is calculated analytically
(numerical solution of integral expressions for Ft, Fr) and not from the
TI MD simulations.
On the other hand the corrections of applying the restraints on fully
interacting ligand (in binding site) denoted in Roux articles as
dGsite_r and dGsite_t are calculated using TI during which the restraint
is slowly eliminated (or applied). This step might be found in previously
mentioned Roux articles
(Biophysical Journal 2006, 91, 2798-2814, J. Phys. Chem. B 2009, 113,
2234–2246, J. Chem. Theory Comput. 2006, 2, 1255-1273).
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 ?
Thanks you in advance for clearing this last point !
Best wishes,
Marek
Dne Thu, 26 Jan 2012 16:43:28 +0100 <steinbrt.rci.rutgers.edu> napsal/-a:
> Hi,
>
>> So I was simply wondering if in the case of setting dvdl_norest = 1
>> (which
>> prevent from including restraint contribution to dV/dl)
>> is all what I have to do to filter-out the restraint influence to dG_dec
>
> That would be all you need to do in *that* step of the calculation. The
> analytical correction does not have any connection to this, but is a
> separate step (without MD simulation) you probably have to do. This part
> would indeed be the correction for restraining translation and rotation
> in
> vacuum, as discussed by Roux et al. You may also have to include a
> correction for indistinguishable microstates when restraining a symmetric
> molecule, as discussed by David Mobley et al.
>
> Kind Regards,
>
> 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 - 09:00:03 PST
