You should check the _MMPBSA complex mdout file. That output file might
have a more helpful error message in it since that is where the error
actually occurred.
-Bill
On Thu, May 21, 2026 at 7:49 AM ElBagoury, Abdulrahman Walid Attia Ibrahim
via AMBER <amber.ambermd.org> wrote:
> Heloo amber members,
>
> I havee been running 6 MD production simulations (3 replicas × 2 docking
> poses) using AMBER for preparation and OpenMM for the production runs (50
> ns each, DCD trajectories). I am now trying to calculate MM-GBSA binding
> free energies using MMPBSA.py and running into an error.
>
> Setup:
> - System: KSHV SOX nuclease (488 residues) + ligand (LIG, residue 491) + 2
> Mg²⁺ ions (residues 489-490)
> - Topology: complex.prmtop generated with tleap (ff14SB)
> - I used ante-MMPBSA.py to generate stripped topologies, keeping Mg²⁺ as
> part of the receptor:
>
> ante-MMPBSA.py -p complex.prmtop -c complex_stripped.prmtop -r
> receptor.prmtop -l ligand.prmtop -n ":491" -s ":WAT,Na+,Cl-"
>
> Verified with cpptraj resinfo:
> - complex_stripped.prmtop: 491 residues (protein 1-488 + MG 489-490 + LIG
> 491)
> - receptor.prmtop: 490 residues (protein 1-488 + MG 489-490)
> - ligand.prmtop: 1 residue (LIG)
>
> Input file (mmpbsa.in):
> &general
> startframe=4113, endframe=5112, interval=1,
> verbose=2, keep_files=0,
> /
> &gb
> igb=5, saltcon=0.150,
> /
>
> The issue is:
>
> (MD_science) mk-avid-workstation.AVID-WW0001:~/MD Sim/MMPBSA/mg_rep1$ cd
> ~/"MD Sim/MMPBSA/mg_rep1"
> MMPBSA.py -O -i ../mmpbsa.in -o MgDock_rep1_RESULTS.dat -eo
> MgDock_rep1_PERFRAME.csv -sp ../mg_complex.prmtop -cp
> ../mg_complex_stripped.prmtop -rp ../mg_receptor.prmtop -lp
> ../mg_ligand.prmtop -y ../mg_rep1.dcd
> Loading and checking parameter files for compatibility...
> cpptraj found! Using
> /home/mk-avid-workstation/miniforge3/envs/MD_science/bin/cpptraj
> mmpbsa_py_energy found! Using
> /home/mk-avid-workstation/miniforge3/envs/MD_science/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/mk-avid-workstation/miniforge3/envs/MD_science/bin/mmpbsa_py_energy
> calculating complex contribution...
> File
> "/home/mk-avid-workstation/miniforge3/envs/MD_science/bin/MMPBSA.py", line
> 101, in <module>
> app.run_mmpbsa() # for membrane runs by automatically setting the
> membrane thickness and location.
> File
> "/home/mk-avid-workstation/miniforge3/envs/MD_science/lib/python3.10/site-packages/MMPBSA_mods/main.py",
> line 225, in run_mmpbsa
> self.calc_list.run(rank, self.stdout)
> File
> "/home/mk-avid-workstation/miniforge3/envs/MD_science/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> line 82, in run
> calc.run(rank, stdout=stdout, stderr=stderr)
> File
> "/home/mk-avid-workstation/miniforge3/envs/MD_science/lib/python3.10/site-packages/MMPBSA_mods/calculation.py",
> line 521, in run
> raise CalcError('%s failed with prmtop %s!' % (self.program,
> CalcError:
> /home/mk-avid-workstation/miniforge3/envs/MD_science/bin/cpptraj failed
> with prmtop ../mg_complex_stripped.prmtop!
>
> 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.
>
> Question is I dont know why that happened so any help would be much
> appreciated.
>
> AmberTools version: 24 (cpptraj V6.24.0)
>
> Thanks in advance for any guidance.
>
> Best regards,
> Abdulrahman
>
>
>
>
> Abdulrahman Walid Attia Ibrahim ElBagoury
> Antivirale und Antivirulenz-Wirkstoffe
>
> Helmholtz-Institut für Pharmazeutische Forschung Saarland
>
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--
Bill Miller III
Associate Professor of Biochemistry
A.T. Still University
417-549-0952
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Received on Thu May 21 2026 - 08:30:03 PDT
