What version of MMPBSA.py are you using? Are you using the version from
AmberTools 1.5?
On Wed, Sep 28, 2011 at 10:43 AM, George Tzotzos <gtzotzos.me.com> wrote:
> Jason
>
> stripping water/ions and merging the trajectory files was done with the
> following input file
>
> trajin prod_2ns.mdcrd
> .................
> trajin prod_20ns.mdcrd
> strip :WAT
> strip :Na+
> trajout prod_0-20ns.mdcrd netcdf
>
> As you can see, netcdf is included
>
> I don't see any great discrepancy in the GB results (see below)
>
> Trajectories stripped of water/ions via the above method submitted to
> MMPBSA.py give
> Generalized Born
> DELTA G binding = -33.4702 +/- 1.8177
> 0.2571
> Poisson Boltzmann
> DELTA G binding = -26.5181 +/- 2.6507
> 0.3749
>
> Trajectories NOT stripped of water/ions PRIOR to being submitted to
> MMPBSA.py
> Generalized Born
> DELTA G binding = -34.3190 +/- 2.0987
> 0.0939
> Poisson Boltzmann
> DELTA G binding = -28.8956 +/- 2.8508
> 0.1275
>
> I've tried to re-run MMPBSA.py including netcdf=1 as per your suggestion
>
> Input file for running PB and GB
> &general
> strip_mdcrd=0
> endframe=50, verbose=1,
> netcdf=1,
> # entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
> I get "Warning: Input error! "netcdf=1" is an invalid option."
>
> I also tried it at &gb and &pb. MMPBSA.py issues the same error message as
> above.
>
>
>
>
> On Sep 28, 2011, at 4:16 PM, Jason Swails wrote:
>
> > 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
> >>>> _______________________________________________
> >>>> 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
> >>> _______________________________________________
> >>> 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
> >>
> >
> >
> >
> > --
> > 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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>
--
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 - 08:30:03 PDT
