Hi, may you share the command that you are using to call MMPBSA.py?
Tomás Cáceres
Bioquímico 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 - 07:00:03 PST
