When MMPBSA.py says it "mmpbsa_py_energy failed with prmtop", I typically
look in the mdout files created by MMPBSA.py for the error message. If
there are any other std out/err files, check those, too. But the error
messages shown are not very indicative of the cause of the error.
-Bill
On Fri, Dec 19, 2025 at 10:04 AM YASHIKA . via AMBER <amber.ambermd.org>
wrote:
> Here is command that I used:
> MMPBSA.py -O -i mmpbsa.in -o mmpbsa_result_wt.dat -cp
> complex_wt_nosolvent.parm7 -rp protein_wt.parm7 -lp sirna_wt.parm7 -y
> traj_wt.mdcrd
> I also tried with the full location of working directory like
> MMPBSA.py -O -i /home/username/Download/184-22/mmpbsa.in....
>
> On Fri, 19 Dec 2025, 20:01 Tomás BenjamÃn Cáceres Madariaga, <
> caceres.tomas.uc.cl> wrote:
>
> > Hi, may you share the command that you are using to call MMPBSA.py?
> >
> > Tomás Cáceres
> > BioquÃmico UC
> > Asistente de Investigación | Laboratorio de Simulación Computacional y
> > Diseño de Fármacos
> > ------------------------------
> > *From:* YASHIKA . via AMBER <amber.ambermd.org>
> > *Sent:* Friday, December 19, 2025 5:30:26 AM
> > *To:* amber.ambermd.org <amber.ambermd.org>
> > *Subject:* [AMBER] Issue with MMGBSA Calculation for Protein–siRNA
> Complex
> >
> > Dear Team,
> >
> > I am performing MMGBSA calculations on a protein–siRNA complex and
> > encountering an error. Below are the details:
> >
> > *System and files:*
> >
> > -
> >
> > *Complex topology (complex_wt_nosolvent.parm7):* 8691 atoms, 502
> > residues, 3 molecules
> > -
> >
> > *Protein topology (protein_wt.parm7):* 7352 atoms, 460 residues, 1
> > molecule
> > -
> >
> > *siRNA topology (sirna_wt.parm7):* 1339 atoms, 42 residues, 2
> molecules
> > -
> >
> > *Trajectory (traj.mdcrd):* 8691 atoms, 502 residues, 3 molecules;
> > stripped of water and ions
> >
> > *MMGBSA input:*
> >
> > &general
> > startframe=1
> > endframe=5000
> > interval=5
> > verbose=2
> > keep_files=0
> > /
> >
> > &gb
> > igb=5
> > saltcon=0.150
> > radiopt=0
> > /
> > *Observed error:*
> > Loading and checking parameter files for compatibility...
> > cpptraj found! Using /home/leena/miniconda3/envs/amber_fix/bin/cpptraj
> > mmpbsa_py_energy found! Using
> > /home/leena/miniconda3/envs/amber_fix/bin/mmpbsa_py_energy
> > Preparing trajectories for simulation...
> > 1000 frames were processed by cpptraj for use in calculation.
> >
> > Running calculations on normal system...
> >
> > Beginning GB calculations with
> > /home/leena/miniconda3/envs/amber_fix/bin/mmpbsa_py_energy
> > calculating complex contribution...
> > File "/home/leena/miniconda3/envs/amber_fix/bin/MMPBSA.py", line 100,
> in
> > <module>
> > app.run_mmpbsa()
> > File
> >
> >
> "/home/leena/miniconda3/envs/amber_fix/lib/python3.10/site-packages/MMPBSA_mods/main.py",
> > line 224, in run_mmpbsa
> > self.calc_list.run(rank, self.stdout)
> > File
> >
> >
> "/home/leena/miniconda3/envs/amber_fix/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> > line 82, in run
> > calc.run(rank, stdout=stdout, stderr=stderr)
> > File
> >
> >
> "/home/leena/miniconda3/envs/amber_fix/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> > line 156, in run
> > raise CalcError('%s failed with prmtop %s!' % (self.program,
> > CalcError: /home/leena/miniconda3/envs/amber_fix/bin/mmpbsa_py_energy
> > failed with prmtop
> >
> >
> /home/leena/Downloads/scmv1/simulation/184_22_out/complex_wt_nosolvent.parm7!
> >
> > Fatal Error!
> > All files have been retained for your error investigation:
> > You should begin by examining the output files of the first failed
> > calculation.
> > Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
> > manual for file naming conventions.
> > Could anyone please advise on what might be causing this failure, or
> > suggest steps to resolve it?
> > Thank You
> > With regards
> > Yashika
> > NSUT, Delhi
> > _______________________________________________
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> >
> >
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--
Bill Miller III
Associate Professor of Biochemistry
A.T. Still University
417-549-0952
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Received on Fri Dec 19 2025 - 11:00:02 PST
