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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Received on Thu Nov 06 2014 - 13:00:04 PST
