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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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CalcError: /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj failed with prmtop COM.prmtop! #262

Closed hima111997 closed 1 year ago

hima111997 commented 2 years ago

Bug summary

i ran a NAMD simulation and converted the files to GROMACS to be able to use gmx_MMPBSA and started the calculation with &gb and QH entropy, however, the calculation stopped before finishing and showed this error: CalcError: /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj failed with prmtop COM.prmtop!

Terminal output

[INFO   ] Starting gmx_MMPBSA v1.5.0.3
[INFO   ] Command-line
  mpirun -np 24 gmx_MMPBSA MPI -O -i mmpbsa.in -cs ../gromacs.pdb -cp ../gromacs.top -ci ../index.ndx -cg 1 13 -ct ../474_mmgbsa_gromacs.xtc -nogui

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /share/apps/conda_envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /share/apps/conda_envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /share/apps/conda_envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /eb/software/GROMACS/2021.3-foss-2021a/bin/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] No receptor structure file was defined. Using ST approach...
[INFO   ] Using receptor structure from complex to generate AMBER topology
[INFO   ] Normal Receptor: Saving group 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] No ligand structure file was defined. Using ST approach...
[INFO   ] Using ligand structure from complex to generate AMBER topology
[INFO   ] Normal Ligand: Saving group 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[INFO   ] Checking the structures consistency...
[INFO   ] 
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[INFO   ] Detected CHARMM topology format...
[INFO   ] Assigning PBRadii mbondi2 to Complex...
[INFO   ] Writing Normal Complex Amber topology...
[INFO   ] No Receptor topology file was defined. Using ST approach...
[INFO   ] Building AMBER Receptor topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Receptor...
[INFO   ] Writing Normal Receptor Amber topology...
[INFO   ] No Ligand topology file was defined. Using ST approach...
[INFO   ] Building AMBER Ligand topology from Complex...
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand Amber topology...
[INFO   ] Selecting residues by distance (10 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 61 residues:
R:P:ALA:233 R:P:PHE:234 R:P:GLU:235 R:P:HSD:236 R:P:ILE:237 R:P:VAL:238 R:P:GLY:240 R:P:ASP:241 R:P:PHE:242 R:P:SER:243
R:P:HSD:244 R:P:SER:245 R:P:GLN:246 R:P:LEU:247 R:P:GLY:248 R:P:GLY:249 R:P:LEU:250 R:P:HSD:251 R:P:LEU:252 R:P:LEU:256
R:P:PHE:270 R:P:ILE:271 R:P:VAL:277 R:P:LYS:278 R:P:ASN:279 R:P:TYR:280 R:P:PHE:281 R:P:ILE:282 R:P:SER:289 R:P:SER:290
R:P:LYS:291 R:P:CYS:292 R:P:VAL:293 R:P:CYS:294 R:P:SER:295 R:P:VAL:296 R:P:ILE:297 R:P:PHE:304 R:P:VAL:315 R:P:VAL:316
R:P:SER:317 R:P:LYS:318 R:P:VAL:319 R:P:ILE:329 R:P:SER:330 R:P:PHE:331 R:P:MET:332 R:P:LEU:333 R:P:TRP:334 R:P:CYS:335
R:P:LYS:336 R:P:HSD:339 R:P:VAL:340 R:P:GLU:341 R:P:THR:342 R:P:PHE:343 R:P:TYR:344 R:P:PRO:345 R:P:LYS:346 R:P:LEU:347
L:H:UNK:348

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[INFO   ] 1000 frames were processed by cpptraj for use in calculation.
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /share/apps/conda_envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
[INFO   ]   calculating receptor contribution...
[INFO   ]   calculating ligand contribution...
[INFO   ] 
Beginning quasi-harmonic calculations with /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj
  File "/share/apps/conda_envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 104, in gmxmmpbsa
    app.run_mmpbsa()
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 202, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 85, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 418, in run
    Calculation.run(self, rank, stdout=self.output)
  File "/share/apps/conda_envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 160, in run
    raise CalcError('%s failed with prmtop %s!' % (self.program,
CalcError: /share/apps/conda_envs/gmxMMPBSA/bin/cpptraj failed with prmtop COM.prmtop!
Error occurred on rank 9.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 9 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[warn] Epoll MOD(1) on fd 56 failed. Old events were 6; read change was 0 (none); write change was 2 (del); close change was 0 (none): Bad file descriptor

gmx_MMPBSA.log

this is the gmx_MMPBSA.log file: gmx_MMPBSA.log

this is the COM.prmtop file: COM.log

Operating system

Linux

gmx_MMPBSA Version

1.5.0.3

Python version

3.9.7

Installation

AmberTools compilation + pip

hima111997 commented 2 years ago

i tried to update to the last stable version but gave the same error when I tried to run the QH entropy

Valdes-Tresanco-MS commented 2 years ago

Can you update from Github and try again?

python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git -U

If you get the same error, please send me the files you are using (*.top+*.itp, *.tpr or *.pdb and 10 frames *.xtc)

hima111997 commented 2 years ago

i updated it but produced the same error input file: mmpbsa.in.log index file: index.ndx.log topology file + parameters: gromacs.top.log pdb file: gromacs.pdb.log first 10 frames: 10frames.xtc.log