Hai,
We are also running with mm-pbsa. The calculations with mm-pbsa are taking
a bit (one of them seemed to stall after a couple of frames, another we
need to increase maxitn it seems), so while those are running we've decided
to do some gbsa tests as well to compare. We are using ambertools 17. I'll
go ahead and run that test to make sure it checks out. Would you recommend
non linear PB for protein DNA by the way?
Joe
-Sent from Android mobile
On Jun 27, 2017 11:27 PM, "Hai Nguyen" <nhai.qn.gmail.com> wrote:
> Hi,
>
> why don't you use mm-pbsa? mm-gbsa is not *that* accurate and I am doubting
> you will get meaningful dG.
>
> per igb=8, which ambertools version you are using? Did this tests pass for
> sander?
>
> cd $AMBERHOME/test/gbneck2nu && make
>
> Hai
>
> On Tue, Jun 27, 2017 at 11:18 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
>
> > Hi all,
> >
> > We're trying to do some tests to compare mm-pbsa and mm-gbsa calculations
> > for a protein/DNA complex. We've now got our mm-pbsa calculations mostly
> > working. For the mm-gbsa calculation, in our &gb section of the
> mmgbsa.in
> > script to MMPBSA.py we are trying igb=5 and igb=8 (both with mbondi2 for
> > the radius set, though we've also tried mbondi3 for the igb=8 case). In
> the
> > igb=5 case we are getting a negative dG, while using igb=8 with either
> > mbondi2 or mbondi3 we are getting very positive dG values. I've seen some
> > previous discussions here about folks having some difficulty with mm-gbsa
> > for protein/nucleic complexes, but it seemed that those were prior to the
> > optimized nucleic gb parameters of igb=8. Can anyone provide any input on
> > whether mm-gbsa is a reasonable approach for relative dG's with either of
> > these GB models? Thanks for your input.
> >
> > Kind regards,
> > Joe
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> >
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Received on Tue Jun 27 2017 - 21:00:03 PDT
