On Tue, Jun 27, 2017 at 11:41 PM, Baker, Joseph <bakerj.tcnj.edu> wrote:
> 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?
>
hi, Ray would be the best person to answer this question.
btw, I am very curious about the comparison between PB and igb8 in your
case once you're done.
cheers
Hai
>
> 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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Received on Tue Jun 27 2017 - 21:30:03 PDT
