Zoey,
Please include the actual file mmpbsa.in - it shows up as a link in your
post and cannot be read.
Also, please include the tleap.in file you used to prepare the system.
Cheers,
Todd
On Wed, Jan 3, 2024 at 4:12 PM Yang, Li-Yen via AMBER <amber.ambermd.org>
wrote:
> 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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>
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Received on Wed Jan 03 2024 - 18:30:02 PST
