Zoey,
The one thing that sticks out to me immediately is that in tleap.in, you're
missing the part for setting PBRadii; I suggest you use one preparatory
tleap script for all of it.
The next part is that you are specifying a salt concentration of 0.15 M in
your tleap.in, but 0.10 in your mmpbsa.in files.
Suggestion: merge all the tleap stuff into one script and fix the mmpbsa.in
parts - you might comment out the PB part for a start, see if you can get
the faster GB part to run.
Cheers,
Todd
On Thu, Jan 4, 2024 at 9:25 AM Yang, Li-Yen <zoeyxyang.gatech.edu> wrote:
> Hi Todd,
>
>
>
> Thanks for the response!
>
>
>
> I’ve attached three files where:
>
>
>
> *tleap.in <http://tleap.in>* is the file I used to generate
> *pro_lig_solvated.parm7*,
>
> (Before running tleap.in, I prepared the pdb file using “pdb4amber --dry
> –nohyd” and substituted the residues names from HIS to HIP, ASP to AS4, GLU
> to GL4 for constant ph simulation)
>
>
>
> *tleap_PBSA.in *is the file I used to generate *pro_lig.parm7, pro.parm7,
> and lig.parm7*.
>
> (Before running tleap_PBSA.in, I prepared the pdb files using “pdb4amber
> --dry –nohyd”)
>
>
>
> *mmpbsa.in <http://mmpbsa.in> *is the file I used to run the mmpbsa
> command.
>
>
>
>
>
> Thanks a lot!
>
>
>
> Best,
>
> Zoey
>
> *From: *Todd Minehardt <todd.minehardt.gmail.com>
> *Date: *Wednesday, January 3, 2024 at 9:03 PM
> *To: *Yang, Li-Yen <zoeyxyang.gatech.edu>, AMBER Mailing List <
> amber.ambermd.org>
> *Subject: *Re: [AMBER] MMPBSA.py error: CalcError: cpptraj failed with
> prmtop pro_lig.parm7!
>
> 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 Thu Jan 04 2024 - 08:00:03 PST
