On Tue, Apr 19, 2016 at 4:55 PM, Cortopassi, Wilian <
wilian.cortopassi.chem.ox.ac.uk> wrote:
> Dear Amber Users,
>
> I am trying to decompose EEL energies per residue without calculating the
> solvation energies (to save some time since I have lots of residues to
> analyse).
>
> I would appreciate if someone could please help me how to turn solvation
> off during MMPBSA or MMGBSA calculations, making it quick to get the EEL
> energies.
>
You can try to set igb=6, but I'm not sure if that will work. But if you
use GB instead of PB, the savings you get by skipping the solvation term is
pretty small. For regular simulations, the added cost of GB over vacuum is
only ~20-30% or so. For decomp with a lot of residue pairs, the
bookkeeping and file I/O is going to be a much larger proportion of the
cost, meaning the difference between GB and vacuum will be even smaller.
All that is to say, that if igb=6 does not work for you, then just pick a
GB model and only look at the electrostatic term, because I guarantee you
will spend orders of magnitude more time looking for a way to skip the GB
calculation than you will spend just doing it.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Apr 19 2016 - 19:00:03 PDT
