Date: Thu, 21 May 2026 12:49:22 +0000
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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