Dear all, Thanks for all replies so far.
I still have a few problems with my MMPBSA calculation of my protein-protein
complex I was hoping for some tips on.
First off all, I noticed that the saltconcentration (saltcon) value greatly
affects the results of my protein-protein delta g values. saltcon=0 gives a
deltaG of +40, while salcon=0.1 gives a deltaG of -60... The default in
MMPBSA is 0, although the tutorial uses saltcon=0.1. Any recommendations on
what would be appropriate to use?
My simulations were carried out with modified Bondi radii (mbondi). MMPBSA
prints a warning that I should use mbondi1 or pbradii. Does it mean that my
simulations shouldnt be used for MMPBSA calculations?
Best regards,
Lars Skjaerven
On Sat, Oct 16, 2010 at 4:45 PM, case <case.biomaps.rutgers.edu> wrote:
> On Fri, Oct 15, 2010, Lars Skjærven wrote:
> >
> > It seems like an infinite cut-off value is common in MMPBSA calculations.
> > I'm doing this on a protein ~3000 residues. Thus the GB calculations with
> > infinite cut off are quite heavy. Would I be in trouble if I reduced the
> > cut-off, to around 12Å?
>
> To add to what has already been said: 12 A is probably too small, and no
> finite value is completely correct. But something like 20-25 Ang will
> probably give you useful results, especially if you use a salt
> concentration
> of 0.1 to 0.2 M.
>
> [I can't prove the above, but salt-screened electrostatics do get very
> small
> once you are well beyond the Debye screening length.]
>
> ....dac
>
>
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Received on Wed Oct 20 2010 - 08:30:05 PDT
