I'm NOT getting messages like
WARNING: INCONSISTENCIES EXIST...
One more thing: I'm using serial MMPBSA for normal calculation and
MMPBSA.MPI for energy decomposition. I don't know if that makes a
difference.
Thanks.
On Tue, May 8, 2012 at 1:42 PM, Jason Swails <jason.swails.gmail.com> wrote:
> I think the PB decomposition and PB "normal" have a different set of
> defaults. This could cause very different total free energies, but the
> binding free energy should be pretty close (since the differences should be
> largely conserved between the complex and receptor).
>
> If I'm misinterpreting your issue, and you're getting a message like
>
> WARNING: INCONSISTENCIES EXIST...
>
> then Bill's response gives the appropriate advice.
>
> A PBSA expert would have to comment more on the changes between decomp PB
> and normal PB.
>
> HTH,
> Jason
>
> On Tue, May 8, 2012 at 2:29 PM, Victor Ma <victordsmagift.gmail.com>
> wrote:
>
> > hi all
> >
> > I'm using Amber 11 and Ambertool 1.5. I noticed that my binding free
> energy
> > calculated from MMPBSA is different when I'm doing pb energy
> decomposition
> > or not. (This does not happen with gb) I further compared each energy
> terms
> > and found out that what makes the difference here is the "EPB" term
> > particularly for the receptor and complex.
> > I'm using ff10 and I added the old param for the Mg since I have that in
> > the system. This is the input I used for energy decomposition.
> > &general
> > startframe=1601, endframe=2000, interval=2,
> > keep_files=2,strip_mask=':WAT:Mg+:Na+',
> > /
> > &pb
> > istrng=0.100,
> > /
> > &decomp
> > idecomp=3, dec_verbose=1, print_res="3; 20-21; 23-27; 71-74; 85-87; 97;
> > 102-110",
> > /
> >
> > I suspect it's the Mg but then gb calculations were fine. Any idea?
> Thanks.
> >
> >
> > Victor
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 08 2012 - 12:00:08 PDT
