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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Received on Fri Dec 19 2025 - 08:30:02 PST
