Thank you very much Jason.
Unfortunately, igb=0 and igb=6 are not available.
The problem is that, for some of my molecules, I have fluorine atoms, which
gives me a "bad atom type f" error when I run GBSA with idecomp. And MMPBSA
calculations are very time consuming for pairwise decomposition.
So I am not entirely sure how to perform pairwise decomposition with fluoro
compounds.
Is there any other way to get the Coulomb energy decomposed by residue
along a MD with Amber?
2016-04-20 2:36 GMT+01:00 Jason Swails <jason.swails.gmail.com>:
> 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 Wed Apr 20 2016 - 04:30:03 PDT
