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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>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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Received on Thu Sep 19 2013 - 08:30:03 PDT
