attached is my MMPBSA_ligand_pb.mdout file
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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Received on Thu Sep 19 2013 - 08:00:05 PDT
