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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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[Bug-gmx_MMPBSA]: cpptraj generate empty mdcrd #475

Open jsjyhzy opened 8 months ago

jsjyhzy commented 8 months ago

Bug summary

dear devs it seems cpptraj was requested to output the frame that not exists, and generate an empty .mdcrd file, eventually making the calculation failed. some lines in _GMXMMPBSA_normal_traj_cpptraj.out is as following

CPPTRAJ: Trajectory Analysis. V5.1.0
    ___  ___  ___  ___
     | \/ | \/ | \/ | 
    _|_/\_|_/\_|_/\_|_

| Date/time: 03/21/24 11:54:38
| Available memory: 109.674 GB

    Reading 'COM.prmtop' as Amber Topology
    Radius Set: H(N)-modified Bondi radii (mbondi2)
INPUT: Reading input from 'STDIN'
  [trajin COM_traj_0.xtc 9900 10000 2]
    Reading 'COM_traj_0.xtc' as Gromacs XTC
Warning: Trajectory box type is 'Cubic' but topology box type is 'None'.
Warning: Setting topology box information from trajectory.

...

  [outtraj _GMXMMPBSA_complex.mdcrd.31 onlyframes 52-52 nobox]
Warning: Format not specified and extension '.31' not recognized. Defaulting to Amber Trajectory.
    Saving frames 52
    Writing '_GMXMMPBSA_complex.mdcrd.31' as Amber Trajectory
    OUTTRAJ: Writing frames associated with topology 'COM.prmtop'

...

Read 51 frames and processed 51 frames.
TIME: Avg. throughput= 27.2959 frames / second.

ACTION OUTPUT:
    OUTTRAJ: '_GMXMMPBSA_complex.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummycomplex.inpcrd': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.0': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.1': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.2': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.3': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.4': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.5': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.6': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.7': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.8': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.9': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.10': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.11': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.12': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.13': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.14': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.15': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.16': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.17': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.18': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.19': Wrote 2 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.20': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.21': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.22': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.23': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.24': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.25': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.26': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.27': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.28': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.29': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_complex.mdcrd.30': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_receptor.pdb': Wrote 1 frames.
    OUTTRAJ: '_GMXMMPBSA_dummyreceptor.inpcrd': Wrote 1 frames.

Terminal output

[INFO   ]   calculating complex contribution...

              0%|          | 0/51 [elapsed: 00:00 remaining: ?]  File "/public/home/neotrident/apps/mmpbsa_1.6.2/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/public/home/neotrident/apps/mmpbsa_1.6.2/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/public/home/neotrident/apps/mmpbsa_1.6.2/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/public/home/neotrident/apps/mmpbsa_1.6.2/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/public/home/neotrident/apps/mmpbsa_1.6.2/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 672, in run
    raise CalcError(f'{self.program} failed with prmtop {self.prmtop}!')
CalcError: /public/home/neotrident/apps/mmpbsa_1.6.2/bin/cpptraj failed with prmtop COM.prmtop!
Error occurred on rank 31.
Exiting. All files have been retained.
Abort(1) on node 31 (rank 31 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 31

gmx_MMPBSA.log

[INFO   ] Starting gmx_MMPBSA v1.6.3
[DEBUG  ] WDIR          : /public/home/neotrident/job/000061/22/aa8d229f-8465-4f80-89f2-c0da5d88c93f/1710900218704/17109003969370655198814129
[DEBUG  ] AMBERHOME     : /public/home/neotrident/apps/mmpbsa_1.6.2
[DEBUG  ] PYTHON EXE    : /public/home/neotrident/apps/mmpbsa_1.6.2/bin/python
[DEBUG  ] PYTHON VERSION: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0]
[DEBUG  ] MPI           : /public/home/neotrident/apps/mmpbsa_1.6.2/bin/mpirun
[DEBUG  ] ParmEd        : 4.2.2
[DEBUG  ] OS PLATFORM   : Linux-3.10.0-957.el7.x86_64-x86_64-with-glibc2.17
[DEBUG  ] OS SYSTEM     : Linux
[DEBUG  ] OS VERSION    : #1 SMP Fri Oct 25 22:34:08 UTC 2019
[DEBUG  ] OS PROCESSOR  : x86_64

[INFO   ] Command-line
  mpirun -np 32 gmx_MMPBSA MPI -O -ct traj.trr -cp topol.top -cs _gmx_mmpbsa_original.pdb -cr reference.pdb -ci index.ndx -cg 0 1 -eo mmpbsa_ana.csv -deo mmpbsa_dec.csv -i mmpbsa.in -nogui

[DEBUG  ] |Input file:
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] |&general
[DEBUG  ] | startframe=9900
[DEBUG  ] | endframe=1000000000
[DEBUG  ] | interval=2
[DEBUG  ] | temperature=298.15
[DEBUG  ] | interaction_entropy=0
[DEBUG  ] | ie_segment=25
[DEBUG  ] | c2_entropy=0
[DEBUG  ] | qh_entropy=0
[DEBUG  ] | exp_ki=0
[DEBUG  ] |
[DEBUG  ] |/
[DEBUG  ] |&gb
[DEBUG  ] | igb=5
[DEBUG  ] | saltcon=0.15
[DEBUG  ] | surfoff=0
[DEBUG  ] | surften=0.0072
[DEBUG  ] | intdiel=1
[DEBUG  ] | extdiel=78.5
[DEBUG  ] |
[DEBUG  ] |/
[DEBUG  ] |&alanine_scanning
[DEBUG  ] | mutant="ALA"
[DEBUG  ] | mutant_res="C:12"
[DEBUG  ] |
[DEBUG  ] |/
[DEBUG  ] |--------------------------------------------------------------
[DEBUG  ] 
[INFO   ] Checking mmpbsa.in input file...
[WARNING] &decomp namelist has not been defined in the input file. Ignoring '-deo' flag... 
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /public/home/neotrident/apps/mmpbsa_1.6.2/bin/cpptraj
[INFO   ] tleap found! Using /public/home/neotrident/apps/mmpbsa_1.6.2/bin/tleap
[INFO   ] parmchk2 found! Using /public/home/neotrident/apps/mmpbsa_1.6.2/bin/parmchk2
[INFO   ] sander found! Using /public/home/neotrident/apps/mmpbsa_1.6.2/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/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...
[DEBUG  ] Running command: echo -e "name 0 GMXMMPBSA_REC\n name 1 GMXMMPBSA_LIG\n  0 | 1\n q\n" | /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f _gmx_mmpbsa_original.pdb
[DEBUG  ]                :-) GROMACS - gmx make_ndx, 2022.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /public/home/neotrident/apps/mmpbsa_1.6.2
[DEBUG  ] Working dir:  /public/home/neotrident/job/000061/22/aa8d229f-8465-4f80-89f2-c0da5d88c93f/1710900218704/17109003969370655198814129
[DEBUG  ] Command line:
[DEBUG  ]   gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f _gmx_mmpbsa_original.pdb
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] Reading structure file
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "The way to succeed is to double your failure rate." (Thomas J. Watson)
[DEBUG  ] 
[DEBUG  ] Going to read 1 old index file(s)
[DEBUG  ] 
[DEBUG  ]   0 new_group_0         :  3020 atoms
[DEBUG  ]   1 new_group_1         :  6367 atoms
[DEBUG  ] 
[DEBUG  ]  nr : group      '!': not  'name' nr name   'splitch' nr    Enter: list groups
[DEBUG  ]  'a': atom       '&': and  'del' nr         'splitres' nr   'l': list residues
[DEBUG  ]  't': atom type  '|': or   'keep' nr        'splitat' nr    'h': help
[DEBUG  ]  'r': residue              'res' nr         'chain' char
[DEBUG  ]  "name": group             'case': case sensitive           'q': save and quit
[DEBUG  ]  'ri': residue index
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] 
[DEBUG  ] > 
[DEBUG  ] Copied index group 0 'GMXMMPBSA_REC'
[DEBUG  ] Copied index group 1 'GMXMMPBSA_LIG'
[DEBUG  ] Merged two groups with OR: 3020 6367 -> 9387
[DEBUG  ] 
[DEBUG  ]   2 GMXMMPBSA_REC_GMXMMPBSA_LIG:  9387 atoms
[DEBUG  ] 
[DEBUG  ] > 
[INFO   ] Normal Complex: Saving group new_group_0_new_group_1 (0_1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG  ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx editconf -f _gmx_mmpbsa_original.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG  ]                :-) GROMACS - gmx editconf, 2022.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /public/home/neotrident/apps/mmpbsa_1.6.2
[DEBUG  ] Working dir:  /public/home/neotrident/job/000061/22/aa8d229f-8465-4f80-89f2-c0da5d88c93f/1710900218704/17109003969370655198814129
[DEBUG  ] Command line:
[DEBUG  ]   gmx editconf -f _gmx_mmpbsa_original.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_COM.pdb
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] Select a group for output:
[DEBUG  ] Group     0 (  GMXMMPBSA_REC) has  3020 elements
[DEBUG  ] Group     1 (  GMXMMPBSA_LIG) has  6367 elements
[DEBUG  ] Group     2 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  9387 elements
[DEBUG  ] Select a group: 
[DEBUG  ] GROMACS reminds you: "I Don't Like Dirt" (The Breeders)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for editconf, to improve usability and utility.
[DEBUG  ] Read 293553 atoms
[DEBUG  ] Volume: 2990.34 nm^3, corresponds to roughly 1345600 electrons
[DEBUG  ] No velocities found
[DEBUG  ] Selected 2: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[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 new_group_0 (0) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG  ] Running command: echo -e "0"| /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx editconf -f _gmx_mmpbsa_original.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_REC.pdb
[DEBUG  ]                :-) GROMACS - gmx editconf, 2022.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /public/home/neotrident/apps/mmpbsa_1.6.2
[DEBUG  ] Working dir:  /public/home/neotrident/job/000061/22/aa8d229f-8465-4f80-89f2-c0da5d88c93f/1710900218704/17109003969370655198814129
[DEBUG  ] Command line:
[DEBUG  ]   gmx editconf -f _gmx_mmpbsa_original.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_REC.pdb
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] Select a group for output:
[DEBUG  ] Group     0 (  GMXMMPBSA_REC) has  3020 elements
[DEBUG  ] Group     1 (  GMXMMPBSA_LIG) has  6367 elements
[DEBUG  ] Group     2 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  9387 elements
[DEBUG  ] Select a group: 
[DEBUG  ] GROMACS reminds you: "The Poodle Chews It" (F. Zappa)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for editconf, to improve usability and utility.
[DEBUG  ] Read 293553 atoms
[DEBUG  ] Volume: 2990.34 nm^3, corresponds to roughly 1345600 electrons
[DEBUG  ] No velocities found
[DEBUG  ] Selected 0: 'GMXMMPBSA_REC'
[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 new_group_1 (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG  ] Running command: echo -e "1"| /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx editconf -f _gmx_mmpbsa_original.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb
[DEBUG  ]                :-) GROMACS - gmx editconf, 2022.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /public/home/neotrident/apps/mmpbsa_1.6.2
[DEBUG  ] Working dir:  /public/home/neotrident/job/000061/22/aa8d229f-8465-4f80-89f2-c0da5d88c93f/1710900218704/17109003969370655198814129
[DEBUG  ] Command line:
[DEBUG  ]   gmx editconf -f _gmx_mmpbsa_original.pdb -n _GMXMMPBSA_COM_index.ndx -o _GMXMMPBSA_LIG.pdb
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] Select a group for output:
[DEBUG  ] Group     0 (  GMXMMPBSA_REC) has  3020 elements
[DEBUG  ] Group     1 (  GMXMMPBSA_LIG) has  6367 elements
[DEBUG  ] Group     2 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  9387 elements
[DEBUG  ] Select a group: 
[DEBUG  ] GROMACS reminds you: "Where all think alike, no one thinks very much." (Walter Lippmann)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for editconf, to improve usability and utility.
[DEBUG  ] Read 293553 atoms
[DEBUG  ] Volume: 2990.34 nm^3, corresponds to roughly 1345600 electrons
[DEBUG  ] No velocities found
[DEBUG  ] Selected 1: 'GMXMMPBSA_LIG'
[INFO   ] Checking the structures consistency...
[INFO   ] Assigning chain ID to structures files according to the reference structure...
[INFO   ] 
[INFO   ] Using topology conversion. Setting radiopt = 0...
[INFO   ] Building Normal Complex Amber topology...
[INFO   ] Detected Amber/OPLS force field 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   ] Building Mutant Complex Topology...
[INFO   ] Mutating C/12 THR by ALA
[INFO   ] Assigning PBRadii mbondi2 to Mutant Complex...
[INFO   ] Writing Mutant Complex AMBER topology...
[INFO   ] Detecting mutation in Receptor. Building Mutant Receptor topology...
[INFO   ] Assigning PBRadii mbondi2 to Mutant Receptor...
[INFO   ] Writing Mutant Receptor AMBER topology...
[INFO   ] Cleaning normal complex trajectories...
[DEBUG  ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx trjconv -f traj.trr -s _gmx_mmpbsa_original.pdb -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ]                :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-:
[DEBUG  ] 
[DEBUG  ] Executable:   /public/home/neotrident/apps/mmpbsa_1.6.2/bin.AVX2_256/gmx
[DEBUG  ] Data prefix:  /public/home/neotrident/apps/mmpbsa_1.6.2
[DEBUG  ] Working dir:  /public/home/neotrident/job/000061/22/aa8d229f-8465-4f80-89f2-c0da5d88c93f/1710900218704/17109003969370655198814129
[DEBUG  ] Command line:
[DEBUG  ]   gmx trjconv -f traj.trr -s _gmx_mmpbsa_original.pdb -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG  ] 
[DEBUG  ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG  ] Group     0 (  GMXMMPBSA_REC) has  3020 elements
[DEBUG  ] Group     1 (  GMXMMPBSA_LIG) has  6367 elements
[DEBUG  ] Group     2 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has  9387 elements
[DEBUG  ] Select a group: trr version: GMX_trn_file (single precision)
[DEBUG  ] 
Reading frame       0 time    0.000   
[DEBUG  ] Setting output precision to 0.001 (nm)
[DEBUG  ] 
Reading frame       1 time   10.000    ->  frame      0 time    0.000      

Reading frame       2 time   20.000    ->  frame      1 time   10.000      

Reading frame       3 time   30.000    ->  frame      2 time   20.000      

Reading frame       4 time   40.000    ->  frame      3 time   30.000      

Reading frame       5 time   50.000    ->  frame      4 time   40.000      

Reading frame       6 time   60.000    ->  frame      5 time   50.000      

Reading frame       7 time   70.000    ->  frame      6 time   60.000      

Reading frame       8 time   80.000    ->  frame      7 time   70.000      

Reading frame       9 time   90.000    ->  frame      8 time   80.000      

Reading frame      10 time  100.000    ->  frame      9 time   90.000      

Reading frame      11 time  110.000    ->  frame     10 time  100.000      

Reading frame      12 time  120.000    ->  frame     11 time  110.000      

Reading frame      13 time  130.000    ->  frame     12 time  120.000      

Reading frame      14 time  140.000    ->  frame     13 time  130.000      

Reading frame      15 time  150.000    ->  frame     14 time  140.000      

Reading frame      16 time  160.000    ->  frame     15 time  150.000      

Reading frame      17 time  170.000    ->  frame     16 time  160.000      

Reading frame      18 time  180.000    ->  frame     17 time  170.000      

Reading frame      19 time  190.000    ->  frame     18 time  180.000      

Reading frame      20 time  200.000    ->  frame     19 time  190.000      

Reading frame      30 time  300.000    ->  frame     29 time  290.000      

Reading frame      40 time  400.000    ->  frame     39 time  390.000      

Reading frame      50 time  500.000    ->  frame     49 time  490.000      

Reading frame      60 time  600.000    ->  frame     59 time  590.000      

Reading frame      70 time  700.000    ->  frame     69 time  690.000      

Reading frame      80 time  800.000    ->  frame     79 time  790.000      

Reading frame      90 time  900.000    ->  frame     89 time  890.000      

Reading frame     100 time 1000.000    ->  frame     99 time  990.000      

Reading frame     110 time 1100.000    ->  frame    109 time 1090.000      

Reading frame     120 time 1200.000    ->  frame    119 time 1190.000      

Reading frame     130 time 1300.000    ->  frame    129 time 1290.000      

Reading frame     140 time 1400.000    ->  frame    139 time 1390.000      

Reading frame     150 time 1500.000    ->  frame    149 time 1490.000      

Reading frame     160 time 1600.000    ->  frame    159 time 1590.000      

Reading frame     170 time 1700.000    ->  frame    169 time 1690.000      

Reading frame     180 time 1800.000    ->  frame    179 time 1790.000      

Reading frame     190 time 1900.000    ->  frame    189 time 1890.000      

Reading frame     200 time 2000.000    ->  frame    199 time 1990.000      

Reading frame     300 time 3000.000    ->  frame    299 time 2990.000      

Reading frame     400 time 4000.000    ->  frame    399 time 3990.000      

Reading frame     500 time 5000.000    ->  frame    499 time 4990.000      

Reading frame     600 time 6000.000    ->  frame    599 time 5990.000      

Reading frame     700 time 7000.000    ->  frame    699 time 6990.000      

Reading frame     800 time 8000.000    ->  frame    799 time 7990.000      

Reading frame     900 time 9000.000    ->  frame    899 time 8990.000      

Reading frame    1000 time 10000.000    ->  frame    999 time 9990.000      

Reading frame    1100 time 11000.000    ->  frame   1099 time 10990.000      

Reading frame    1200 time 12000.000    ->  frame   1199 time 11990.000      

Reading frame    1300 time 13000.000    ->  frame   1299 time 12990.000      

Reading frame    1400 time 14000.000    ->  frame   1399 time 13990.000      

Reading frame    1500 time 15000.000    ->  frame   1499 time 14990.000      

Reading frame    1600 time 16000.000    ->  frame   1599 time 15990.000      

Reading frame    1700 time 17000.000    ->  frame   1699 time 16990.000      

Reading frame    1800 time 18000.000    ->  frame   1799 time 17990.000      

Reading frame    1900 time 19000.000    ->  frame   1899 time 18990.000      

Reading frame    2000 time 20000.000    ->  frame   1999 time 19990.000      

Reading frame    3000 time 30000.000    ->  frame   2999 time 29990.000      

Reading frame    4000 time 40000.000    ->  frame   3999 time 39990.000      

Reading frame    5000 time 50000.000    ->  frame   4999 time 49990.000      

Reading frame    6000 time 60000.000    ->  frame   5999 time 59990.000      

Reading frame    7000 time 70000.000    ->  frame   6999 time 69990.000      

Reading frame    8000 time 80000.000    ->  frame   7999 time 79990.000      

Reading frame    9000 time 90000.000    ->  frame   8999 time 89990.000      

Reading frame   10000 time 100000.000    ->  frame   9999 time 99990.000      

Last frame      10000 time 100000.000   
[DEBUG  ] Last written: frame  10000 time 100000.000
[DEBUG  ] 
[DEBUG  ] 
[DEBUG  ] GROMACS reminds you: "The Feeling of Power was Intoxicating, Magic" (Frida Hyvonen)
[DEBUG  ] 
[DEBUG  ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG  ] Select group for output
[DEBUG  ] Selected 2: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO   ] Building AMBER topologies from GROMACS files... Done.

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

[INFO   ] Mutating trajectories...
[INFO   ] 51 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 32 CPUs...
[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /public/home/neotrident/apps/mmpbsa_1.6.2/bin/sander
[INFO   ]   calculating complex contribution...

Operating system

No response

gmx_MMPBSA Version

No response

Python version

No response

Installation

None

marioernestovaldes commented 8 months ago

Have you tried without using multiprocessing with mpirun? Or with fewer cores?