I noticed that you are running with AmberTools 12... What happens if you
upgrade to AmberTools 13 (with all available patches)?
On Thu, Sep 19, 2013 at 11:18 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
sumra.msbi30.iiu.edu.pk> wrote:
> attached are required files
>
> Regards
>
> Sumra Wajid Abbasi
> PhD Scholar
> Computational Biology Lab, National Center for Bioinformatics
> Quaid-e-Azam University, Islamabad-45320 Pakistan.
>
>
> On Thu, Sep 19, 2013 at 3:07 PM, Jason Swails <jason.swails.gmail.com
> >wrote:
>
> > On Thu, Sep 19, 2013 at 10:54 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09 <
> > sumra.msbi30.iiu.edu.pk> wrote:
> >
> > > attached is my MMPBSA_ligand_pb.mdout file
> > >
> >
> > Every snapshot is NaN. Can you send me the _MMPBSA_ligand.mdcrd file and
> > the corresponding topology file off-list, please?
> >
> >
> > >
> > > Regards
> > >
> > > Sumra Wajid Abbasi
> > > PhD Scholar
> > > Computational Biology Lab, National Center for Bioinformatics
> > > Quaid-e-Azam University, Islamabad-45320 Pakistan.
> > >
> > >
> > > On Thu, Sep 19, 2013 at 7:49 PM, Jason Swails <jason.swails.gmail.com
> > > >wrote:
> > >
> > > > On Thu, Sep 19, 2013 at 9:56 AM, Sumra Wajid Abbasi 30-FBAS/MSBI/F09
> <
> > > > sumra.msbi30.iiu.edu.pk> wrote:
> > > >
> > > > > Dear Jason
> > > > > My input file consists of following parameters:
> > > > > Input file for running PB and GB
> > > > > &general
> > > > >
> > > > > startframe=1, endframe=50, interval=1,
> > > > >
> > > > > verbose=2, keep_files=0,
> > > > >
> > > > >
> > > >
> > > > When you are debugging, you should set keep_files at its default, or
> > set
> > > it
> > > > to 2. keep_files=0 means discard all intermediate files (which makes
> > > > debugging harder).
> > > >
> > > > [snip]
> > > > >
> > > > > Ligand:
> > > > > Energy Component Average Std. Dev. Std.
> > Err.
> > > of
> > > > > Mean
> > > > >
> > > > >
> > > >
> > >
> >
> -------------------------------------------------------------------------------
> > > > > BOND 22.8209 3.7323
> > > > > 0.5278
> > > > > ANGLE 67.2316 5.6725
> > > > > 0.8022
> > > > > DIHED 57.9771 3.3766
> > > > > 0.4775
> > > > > VDWAALS -21.1078 1.7341
> > > > > 0.2452
> > > > > 1-4 VDW 23.3635 2.0523
> > > > > 0.2902
> > > > > EPB nan nan
> > > > > nan
> > > > > ENPOLAR 97.8510 0.8688
> > > > > 0.1229
> > > > >
> > > > > G gas 150.2853 7.8027
> > > > > 1.1035
> > > > > G solv nan nan
> > > > > nan
> > > > >
> > > > > TOTAL nan nan
> > > > > nan
> > > > >
> > > >
> > > > So this is definitely your problem. Somewhere the polar solvation
> free
> > > > energy is hitting some type of undefined behavior, but I'm not sure
> > why.
> > > > Can you send me your _MMPBSA_ligand_pb.mdout.* files? (You may have
> to
> > > > re-run it if all of your files were deleted).
> > > >
> > > > That said, the picture you showed would cause problems in all of the
> > > energy
> > > > terms for each system (GB and PB alike) -- it would certainly not
> > > manifest
> > > > as a NaN in EPB. With the exception of EPB, all of the energy terms
> > are
> > > > far too reasonable to have come from a molecule as warped as the one
> > you
> > > > showed a picture of.
> > > >
> > > > My guess is that you are not visualizing the trajectory properly
> > > (MMPBSA.py
> > > > strips out box information, so make sure you're not specifying
> > > trajectories
> > > > with box info). Hopefully your files can shed some light about what
> is
> > > > happening...
> > > >
> > > > when i visualized prmtop and MMBPSA.py generated mdcrds i found
> > > > > a distorted ligand. i also tried MMPBSA.pl but no results.
> > > > >
> > > > > kindly attached image of ligand hopefully these would be helpful
> for
> > > you
> > > > >
> > > >
> > > > HTH,
> > > > Jason
> > > >
> > > > --
> > > > Jason M. Swails
> > > > BioMaPS,
> > > > Rutgers University
> > > > Postdoctoral Researcher
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> > > >
> > >
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> > >
> >
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 19 2013 - 12:30:04 PDT
