On Wed, Dec 29, 2010 at 8:31 AM, Catein Catherine <askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
> Can I run the trajectory in implicit solvent and then do the MM-GBSA/PBSA
> analysis using the implicit trajectory? Or is it a must to run the MD in
> explicit solvent?
>
If you can afford it, explicit solvent is typically considered to be more
accurate, though the calculation is more expensive (much more so for some of
the advanced sampling techniques like REMD and TI). There is certainly
nothing wrong with doing it in implicit solvent, though (unless of course
implicit solvent is shown to produce horrible results, as with nucleic acids
in many cases). MMPBSA.py has an option (strip_mdcrd=0) that will avoid
having to strip the trajectory file (appropriate for trajectories that have
already been preprocessed to remove the waters as well as implicit-solvent
simulations).
Good luck,
Jason
>
> Best regards,
> Catherine
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Dec 29 2010 - 11:00:03 PST
