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 Sat Oct 16 2010 - 08:00:05 PDT
