Xiaolin
The MM-GBSA method uses a generalised Born method within AMBER to
calculate solvation energy (read the MM-PBSA part of the manual).
The other option is indeed to use Delphi to calculate solvation
energies. I have no experience with GB calculations, but can tell
you that generally you will need to parameterise any new GB
parameters that you might need, against Poisson Boltzmann
calculations (Delphi). PB calculations are more accurate. The
program is not too expensive, and is probably worthwhile
purchasing, if you intend to do lots of solvation energy type
calculations.
Samantha
Xiaolin Chuang wrote:
>
> Dear Amber users,
>
> I would like to calculate solvation energy of DNA. Can amber package do
> this? Any suggestion would be appreciated.
>
> Sincerely yours,
> Xiaolin
>
> _________________________________________________________________
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Received on Wed Jul 25 2001 - 23:54:11 PDT
