When you stripped all waters and everything else, did you do anything else?
(For instance, did you align via RMSD, etc.)?
Here is my suggestion. Work *completely* in NetCDF trajectories. I don't
know if your initial trajectories are NetCDF (I would strongly encourage you
to use NetCDF if you're not). Make sure the stripped trajectory that you
make is created as a NetCDF trajectory. Then, use netcdf=1 in your
MMPBSA.py input file. This will force MMPBSA.py to use NetCDF for the
temporary internal files.
I'd be curious to see if the (vastly) increased precision of a NetCDF
trajectory can account for some of this difference...
Also, you never say whether the discrepancy arises in the PB results or GB
results (I would expect the PB results, yes?).
All the best,
Jason
On Wed, Sep 28, 2011 at 9:33 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Bill
>
> Thanks for the prompt reply
>
> Run1: mmpbsa.in
>
> Input file for running PB and GB
> &general
> endframe=50, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
>
> Run 2: mmpbsa.in
>
> Input file for running PB and GB
> &general
> strip_mdcrd=0
> endframe=50, verbose=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
>
> On Sep 28, 2011, at 3:27 PM, Bill Miller III wrote:
>
> > What does your mmpbsa.in file look like? Are you calculating the binding
> > energy for all frames or only a select number of frames? If you are only
> > using a select number of frames I would bet that the two methods selected
> > different frames to evaluate and that resulted in the discrepancy that
> you
> > are reporting here.
> >
> > -Bill
> >
> > On Wed, Sep 28, 2011 at 9:20 AM, George Tzotzos <gtzotzos.me.com> wrote:
> >
> >> Hi everybody,
> >>
> >> I'd appreciate any comments / help on the discrepancies shown below.
> >>
> >> I run MMPBSA.py on the same 20ns trajectory twice.
> >>
> >> 1. Run 1
> >>
> >> mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS.dat -sp
> >> complex_solv.prmtop -cp complex.prmtop -rp receptor.prmtop -lp
> ligand.prmtop
> >> -y *.mdcrd
> >>
> >> *.mdcrd represents 10x2ns trajectories
> >>
> >> 2. Run 2
> >>
> >> Step 1. merge the 2ns trajectories into a 20ns.mdcrd while stripping
> waters
> >> and ions
> >>
> >> Step 2. generated new topology files for complex, receptor and ligand
> >>
> >> run MMPBSA.py
> >>
> >> mpirun -np 12 MMPBSA.py.MPI -O -i mmpbsa.in -o RESULTS.dat -cp
> >> comp_new.prmtop -rp rec_new.prmtop -lp lig_new.prmtop -y *.mdcrd
> >>
> >> Result of Run1.
> >>
> >> DELTA G binding = -28.8956 +/- 2.8508
> >> 0.1275
> >>
> >> Result of Run2
> >>
> >> DELTA G binding = -26.5181 +/- 2.6507
> >> 0.3749
> >> _______________________________________________
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> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Bill Miller III
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Graduate Student
> > 352-392-6715
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Sep 28 2011 - 07:30:04 PDT
