Then this sounds like what Jason was alluding to. Some of the PB default
parameters for normal PB calculations are probably different than the
default parameters for decomposition PB calculations. You will have to
consult the manual, code, or a PB Amber developer for more information if
you want it.
-Bill
On Tue, May 8, 2012 at 2:52 PM, Victor Ma <victordsmagift.gmail.com> wrote:
> 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
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Tue May 08 2012 - 12:00:11 PDT
