OK thanks for this additional although a little pessimistic :)) info !
In a World of approximations one has to simply use the least
approximative route which is available. That's what I am trying to do (
hopefully :)) )
Best wishes,
Marek
Dne Wed, 15 Jun 2011 17:36:21 +0200 <steinbrt.rci.rutgers.edu> napsal/-a:
> Hi Marek,
>
>> But this is not my case. Having significant part of molecule hydrophobic
>> there is significant change
>> in molecular structure upon it's solvation so the change in internal
>> energy (EL., VDW, bond ...) is not
>> negligible comparing to solvent-solute part.
>
> I see... For that system, using MMPBSA makes sense of course. What I was
> trying to say before is, if your molecule changes shape a lot during
> solvation, it is quite likely that the forcefield will not give you a
> good
> conformational ensemble for the vacuum state, to give just one example,
> partial charges are derived specifically for the solvated system.
>
> 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 Wed Jun 15 2011 - 09:00:08 PDT
