Dear Amber community,
I am trying to use MMPBSA.py to calculate binding free energy of a protein-protein complex following this tutorial: https://ambermd.org/tutorials/advanced/tutorial3/py_script/index.php
I used the same mmpbsa.in file and ran the command provided by the tutorial (I used parm7 instead of promtop, not sure if that will cause any issue?):
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp pro_lig_solvated.parm7 -cp pro_lig.parm7 -rp pro.parm7 -lp lig.parm7 -y prod.nc
I am getting the following error:
“Loading and checking parameter files for compatibility...
50 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with (PATH)/mmpbsa_py_energy
calculating complex contribution...
File (PATH)/amber22/bin/MMPBSA.py", line 100, in <module>
app.run_mmpbsa()
File (PATH)/amber22/lib/python3.10/site-packages/MMPBSA_mods/main.py", line 224, in run_mmpbsa
self.calc_list.run(rank, self.stdout)
File (PATH)/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 82, in run
calc.run(rank, stdout=stdout, stderr=stderr)
File (PATH)/amber22/lib/python3.10/site-packages/MMPBSA_mods/calculation.py", line 519, in run
raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: (PATH)/amber22/bin/cpptraj failed with prmtop pro_lig.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.”
I’m not sure how to figure out what’s going wrong from the error above. The following are the file names that were outputted from the command.
However, there is no error message from those files.
Can anyone point me to find out what may be going wrong?
_MMPBSA_dummycomplex.inpcrd
_MMPBSA_dummyligand.inpcrd
_MMPBSA_dummyreceptor.inpcrd
_MMPBSA_gb.mdin
_MMPBSA_ligand.mdcrd.0
_MMPBSA_ligand.pdb
_MMPBSA_normal_traj_cpptraj.out
_MMPBSA_pb.mdin
_MMPBSA_pb.mdin2
_MMPBSA_receptor.mdcrd.0
_MMPBSA_receptor.pdb
_MMPBSA_complex_gb.mdout.0
_MMPBSA_complex.mdcrd.0
_MMPBSA_complex.pdb
Thank you!
Best,
Zoey
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Received on Wed Jan 03 2024 - 14:30:02 PST
