Try upgrading to AmberTools 1.5 and see if you get the same issues.
-Bill
On Wed, Sep 28, 2011 at 11:44 AM, George Tzotzos <gtzotzos.me.com> wrote:
> No, I'm using the AmberTools 1.4 version
>
>
> On Sep 28, 2011, at 5:23 PM, Jason Swails wrote:
>
> > 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
> >>
> >> _______________________________________________
> >> 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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> 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 Wed Sep 28 2011 - 09:30:02 PDT
