On Thu, Nov 6, 2014 at 3:24 PM, Wong, Sook (NIH/NCATS) [V] <
sook.wong.nih.gov> wrote:
> Good to know Jason. I am trying the python script now and currently
> holding on the following for few minutes already without seeing any changes:
>
> [* binding_MMPBSA.py]$ MMPBSA.py -O -i mmpbsa.in -o
> FINAL_RESULTS_MMPBSA.dat -sp com.prmtop -cp com_vac.prmtop -rp
> rec_vac.prmtop -lp lig_vac.prmtop -y galk.clean.mdcrd
> Loading and checking parameter files for compatibility...
> mmpbsa_py_energy found! Using /*/amber14/bin/mmpbsa_py_energy
> cpptraj found! Using /*/amber14/bin/cpptraj
> Preparing trajectories for simulation...
>
> Any idea?
>
​Does your trajectory file have a lot of frames? I don't see any
indication that an error has occurred.
Try analyzing only one or two frames to make sure it works.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Nov 06 2014 - 13:00:03 PST
