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
> > _______________________________________________
> > 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 - 08:30:03 PDT
