suggests you don't have libnetcdf installed, or not the right version for
your AMBER install.
Are you in linux? If so can you use your package manager to install
libnetcdf?
Or maybe you already have the library but it's in an unexpected location
and needs to be added to the LD_LIBRARY_PATH environment variable.
Did you have a problem installing the latest AmberTools?
On Thu, Nov 6, 2014 at 3:54 PM, Wong, Sook (NIH/NCATS) [V] <
sook.wong.nih.gov> wrote:
> While trying with 2 trajectories, I have the following:
>
> [*1 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...
> 2 frames were processed by cpptraj for use in calculation.
>
> Running calculations on normal system...
>
> Beginning GB calculations with /*/amber14/bin/mmpbsa_py_energy
> calculating complex contribution...
> /*/amber14/bin/mmpbsa_py_energy: error while loading shared libraries:
> libnetcdf.so.7: cannot open shared object file: No such file or directory
> File "/*/amber14/bin/MMPBSA.py", line 96, in <module>
> app.run_mmpbsa()
> File "/*/amber14/bin/MMPBSA_mods/main.py", line 218, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File "/*/amber14/bin/MMPBSA_mods/calculation.py", line 79, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File "/*/amber14/bin/MMPBSA_mods/calculation.py", line 148, in run
> self.prmtop))
> CalcError: / */amber14/bin/mmpbsa_py_energy failed with prmtop
> com_vac.prmtop!
> Exiting. All files have been retained.
>
> Does this have to do with the Amber14 set up?
>
> Thank you.
> -Sook
>
> -----Original Message-----
> From: Jason Swails [mailto:jason.swails.gmail.com]
> Sent: Thursday, November 06, 2014 3:35 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] Binding energy using mm_pbsa.pl
>
> 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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>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Thu Nov 06 2014 - 14:00:03 PST
