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 - 08:00:04 PDT
