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[Bug-gmx_MMPBSA]: failed with prmtop COM.prmtop! #529

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Simon-dumplings opened this issue Aug 7, 2024 · 0 comments
Open

[Bug-gmx_MMPBSA]: failed with prmtop COM.prmtop! #529

Simon-dumplings opened this issue Aug 7, 2024 · 0 comments

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@Simon-dumplings
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Bug summary

When I use MMPBSA to calculate the binding energy, I get the error "failed with prmtop COM.prmtop!"

Terminal output

(gmxMMPBSA) root@yutong-virtual-machine:~/PBSA/╫╘╩╔/Beclin1# mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -cp complex.top -ci index.ndx -cg 1 13 -ct md-nopbc.xtc -o energy.dat -do decomp.dat -nogui && gmx_MMPBSA --clean
[INFO   ] Starting gmx_MMPBSA v1.6.3
[INFO   ] Command-line
  mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -cp complex.top -ci index.ndx -cg 1 13 -ct md-nopbc.xtc -o energy.dat -do decomp.dat -nogui

[INFO   ] Checking mmpbsa.in input file...
[INFO   ] Checking mmpbsa.in input file...Done.

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /root/anaconda3/envs/gmxMMPBSA/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...
[INFO   ] Normal Complex: Saving group Protein_MOL (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 Protein (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 MOL (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 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   ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 13 residues:
R:A:PRO:11  R:A:PHE:12  R:A:GLU:13  R:A:TYR:14  R:A:ARG:15  R:A:LYS:16  R:A:LYS:17  R:A:GLU:18  R:A:LYS:156 R:A:ALA:157
R:A:ARG:158 R:A:LYS:235 L:B:MOL:236

[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   ] 101 frames were processed by cpptraj for use in calculation.
[INFO   ] Starting calculations in 8 CPUs...
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.

[INFO   ] Running calculations on normal system...
[INFO   ] Beginning GB calculations with /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
            100%|##########| 101/101 [elapsed: 05:02 remaining: 00:00]
[INFO   ]   calculating receptor contribution...
            100%|##########| 101/101 [elapsed: 11:27 remaining: 00:00]
[INFO   ]   calculating ligand contribution...
            100%|##########| 101/101 [elapsed: 00:11 remaining: 00:00]
[INFO   ] Beginning PB calculations with /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ]   calculating complex contribution...
              0%|          | 0/101 [elapsed: 00:00 remaining: ?][ERROR  ] CalcError 

/root/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
	
If you are using sander and PB calculation, check the *.mdout files to get the sander error


Check the gmx_MMPBSA.log file to report the problem.
  File "/root/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 101, in gmxmmpbsa
    app.run_mmpbsa()
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 205, in run_mmpbsa
    self.calc_list.run(rank, self.stdout)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 142, in run
    calc.run(rank, stdout=stdout, stderr=stderr)
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/calculation.py", line 625, in run
    GMXMMPBSA_ERROR('%s failed with prmtop %s!\n\t' % (self.program, self.prmtop) +
  File "/root/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
CalcError: 

/root/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!
	
If you are using sander and PB calculation, check the *.mdout files to get the sander error


Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 1.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 1

gmx_MMPBSA.log

[ERROR ] CalcError

/root/anaconda3/envs/gmxMMPBSA/bin/sander failed with prmtop COM.prmtop!

If you are using sander and PB calculation, check the *.mdout files to get the sander error

Check the gmx_MMPBSA.log file to report the problem.
: 3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:45:29) [GCC 10.4.0]
[DEBUG ] MPI : /root/anaconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG ] ParmEd : 4.2.2
[DEBUG ] OS PLATFORM : Linux-5.15.0-117-generic-x86_64-with-glibc2.31
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #127~20.04.1-Ubuntu SMP Thu Jul 11 15:36:12 UTC 2024
[DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line
mpirun -np 8 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -cp complex.top -ci index.ndx -cg 1 13 -ct md-nopbc.xtc -o energy.dat -do decomp.dat -nogui

[DEBUG ] |Input file:
[DEBUG ] |--------------------------------------------------------------
[DEBUG ] |Input file generated by gmx_MMPBSA (v1.6.3)
[DEBUG ] |Be careful with the variables you modify, some can have severe consequences on the results you obtain.
[DEBUG ] |
[DEBUG ] |# General namelist variables
[DEBUG ] |&general
[DEBUG ] | sys_name = "" # System name
[DEBUG ] | startframe = 1 # First frame to analyze
[DEBUG ] | endframe = 9999999 # Last frame to analyze
[DEBUG ] | interval = 1 # Number of frames between adjacent frames analyzed
[DEBUG ] | forcefields = "oldff/leaprc.ff99SB,leaprc.gaff" # Define the force field to build the Amber topology
[DEBUG ] | ions_parameters = 1 # Define ions parameters to build the Amber topology
[DEBUG ] | PBRadii = 3 # Define PBRadii to build amber topology from GROMACS files
[DEBUG ] | temperature = 298.15 # Temperature
[DEBUG ] | qh_entropy = 0 # Do quasi-harmonic calculation
[DEBUG ] | interaction_entropy = 0 # Do Interaction Entropy calculation
[DEBUG ] | ie_segment = 25 # Trajectory segment to calculate interaction entropy
[DEBUG ] | c2_entropy = 0 # Do C2 Entropy calculation
[DEBUG ] | assign_chainID = 0 # Assign chains ID
[DEBUG ] | exp_ki = 0.0 # Experimental Ki in nM
[DEBUG ] | full_traj = 0 # Print a full traj. AND the thread trajectories
[DEBUG ] | gmx_path = "" # Force to use this path to get GROMACS executable
[DEBUG ] | keep_files = 2 # How many files to keep after successful completion
[DEBUG ] | netcdf = 0 # Use NetCDF intermediate trajectories
[DEBUG ] | solvated_trajectory = 1 # Define if it is necessary to cleanup the trajectories
[DEBUG ] | verbose = 1 # How many energy terms to print in the final output
[DEBUG ] |/
[DEBUG ] |
[DEBUG ] |# (AMBER) Generalized-Born namelist variables
[DEBUG ] |&gb
[DEBUG ] | igb = 5 # GB model to use
[DEBUG ] | intdiel = 1.0 # Internal dielectric constant for sander
[DEBUG ] | extdiel = 78.5 # External dielectric constant for sander
[DEBUG ] | saltcon = 0.0 # Salt concentration (M)
[DEBUG ] | surften = 0.0072 # Surface tension
[DEBUG ] | surfoff = 0.0 # Surface tension offset
[DEBUG ] | molsurf = 0 # Use Connelly surface ('molsurf' program)
[DEBUG ] | msoffset = 0.0 # Offset for molsurf calculation
[DEBUG ] | probe = 1.4 # Solvent probe radius for surface area calc
[DEBUG ] | ifqnt = 0 # Use QM on part of the system
[DEBUG ] | qm_theory = "" # Semi-empirical QM theory to use
[DEBUG ] | qm_residues = "" # Residues to treat with QM
[DEBUG ] | com_qmmask = "" # Mask specifying the quantum atoms in complex
[DEBUG ] | rec_qmmask = "" # Mask specifying the quantum atoms in receptor
[DEBUG ] | lig_qmmask = "" # Mask specifying the quantum atoms in ligand
[DEBUG ] | qmcharge_com = 0 # Charge of QM region in complex
[DEBUG ] | qmcharge_lig = 0 # Charge of QM region in ligand
[DEBUG ] | qmcharge_rec = 0 # Charge of QM region in receptor
[DEBUG ] | qmcut = 9999.0 # Cutoff in the QM region
[DEBUG ] | scfconv = 1e-08 # Convergence criteria for the SCF calculation, in kcal/mol
[DEBUG ] | peptide_corr = 0 # Apply MM correction to peptide linkages
[DEBUG ] | writepdb = 1 # Write a PDB file of the selected QM region
[DEBUG ] | verbosity = 0 # Controls the verbosity of QM/MM related output
[DEBUG ] | alpb = 0 # Use Analytical Linearized Poisson-Boltzmann (ALPB)
[DEBUG ] | arad_method = 1 # Selected method to estimate the effective electrostatic size
[DEBUG ] |/
[DEBUG ] |
[DEBUG ] |# (AMBER) Possion-Boltzmann namelist variables
[DEBUG ] |&pb
[DEBUG ] | ipb = 2 # Dielectric model for PB
[DEBUG ] | inp = 1 # Nonpolar solvation method
[DEBUG ] | sander_apbs = 0 # Use sander.APBS?
[DEBUG ] | indi = 1.0 # Internal dielectric constant
[DEBUG ] | exdi = 80.0 # External dielectric constant
[DEBUG ] | emem = 4.0 # Membrane dielectric constant
[DEBUG ] | smoothopt = 1 # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary
[DEBUG ] | istrng = 0.0 # Ionic strength (M)
[DEBUG ] | radiopt = 1 # Use optimized radii?
[DEBUG ] | prbrad = 1.4 # Probe radius
[DEBUG ] | iprob = 2.0 # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer
[DEBUG ] | sasopt = 0 # Molecular surface in PB implict model
[DEBUG ] | arcres = 0.25 # The resolution (Å) to compute solvent accessible arcs
[DEBUG ] | memopt = 0 # Use PB optimization for membrane
[DEBUG ] | mprob = 2.7 # Membrane probe radius in Å
[DEBUG ] | mthick = 40.0 # Membrane thickness
[DEBUG ] | mctrdz = 0.0 # Distance to offset membrane in Z direction
[DEBUG ] | poretype = 1 # Use exclusion region for channel proteins
[DEBUG ] | npbopt = 0 # Use NonLinear PB solver?
[DEBUG ] | solvopt = 1 # Select iterative solver
[DEBUG ] | accept = 0.001 # Sets the iteration convergence criterion (relative to the initial residue)
[DEBUG ] | linit = 1000 # Number of SCF iterations
[DEBUG ] | fillratio = 4.0 # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute
[DEBUG ] | scale = 2.0 # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å)
[DEBUG ] | nbuffer = 0.0 # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface
[DEBUG ] | nfocus = 2 # Electrostatic focusing calculation
[DEBUG ] | fscale = 8 # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation
[DEBUG ] | npbgrid = 1 # Sets how often the finite-difference grid is regenerated
[DEBUG ] | bcopt = 5 # Boundary condition option
[DEBUG ] | eneopt = 2 # Compute electrostatic energy and forces
[DEBUG ] | frcopt = 0 # Output for computing electrostatic forces
[DEBUG ] | scalec = 0 # Option to compute reaction field energy and forces
[DEBUG ] | cutfd = 5.0 # Cutoff for finite-difference interactions
[DEBUG ] | cutnb = 0.0 # Cutoff for nonbonded interations
[DEBUG ] | nsnba = 1 # Sets how often atom-based pairlist is generated
[DEBUG ] | decompopt = 2 # Option to select different decomposition schemes when INP = 2
[DEBUG ] | use_rmin = 1 # The option to set up van der Waals radii
[DEBUG ] | sprob = 0.557 # Solvent probe radius for SASA used to compute the dispersion term
[DEBUG ] | vprob = 1.3 # Solvent probe radius for molecular volume (the volume enclosed by SASA)
[DEBUG ] | rhow_effect = 1.129 # Effective water density used in the non-polar dispersion term calculation
[DEBUG ] | use_sav = 1 # Use molecular volume (the volume enclosed by SASA) for cavity term calculation
[DEBUG ] | cavity_surften = 0.0378 # Surface tension
[DEBUG ] | cavity_offset = -0.5692 # Offset for nonpolar solvation calc
[DEBUG ] | maxsph = 400 # Approximate number of dots to represent the maximum atomic solvent accessible surface
[DEBUG ] | maxarcdot = 1500 # Number of dots used to store arc dots per atom
[DEBUG ] | npbverb = 0 # Option to turn on verbose mode
[DEBUG ] |/
[DEBUG ] |
[DEBUG ] |# Decomposition namelist variables
[DEBUG ] |&decomposition
[DEBUG ] | idecomp = 2 # Which type of decomposition analysis to do
[DEBUG ] | dec_verbose = 0 # Control energy terms are printed to the output
[DEBUG ] | print_res = "within 6" # Which residues to print decomposition data for
[DEBUG ] | csv_format = 1 # Write decomposition data in CSV format
[DEBUG ] |/
[DEBUG ] |
[DEBUG ] |--------------------------------------------------------------
[DEBUG ]
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /root/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /root/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /root/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /root/anaconda3/envs/gmxMMPBSA/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 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2021.3-bioconda (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx make_ndx, version 2021.3-bioconda
[DEBUG ] Executable: /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /root/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /root/PBSA/╫╘╩╔/Beclin1
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Louis Pasteur's theory of germs is ridiculous fiction." (Pierre Pachet, Professor of Physiology at Toulouse, 1872)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 63006 atoms
[DEBUG ] 1 Protein : 3972 atoms
[DEBUG ] 2 Protein-H : 1997 atoms
[DEBUG ] 3 C-alpha : 235 atoms
[DEBUG ] 4 Backbone : 705 atoms
[DEBUG ] 5 MainChain : 939 atoms
[DEBUG ] 6 MainChain+Cb : 1166 atoms
[DEBUG ] 7 MainChain+H : 1158 atoms
[DEBUG ] 8 SideChain : 2814 atoms
[DEBUG ] 9 SideChain-H : 1058 atoms
[DEBUG ] 10 Prot-Masses : 3972 atoms
[DEBUG ] 11 non-Protein : 59034 atoms
[DEBUG ] 12 Other : 80 atoms
[DEBUG ] 13 MOL : 80 atoms
[DEBUG ] 14 CL : 4 atoms
[DEBUG ] 15 Water : 58950 atoms
[DEBUG ] 16 SOL : 58950 atoms
[DEBUG ] 17 non-Water : 4056 atoms
[DEBUG ] 18 Ion : 4 atoms
[DEBUG ] 19 MOL : 80 atoms
[DEBUG ] 20 CL : 4 atoms
[DEBUG ] 21 Water_and_ions : 58954 atoms
[DEBUG ] 22 Protein_MOL : 4052 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 1 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 13 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 3972 80 -> 4052
[DEBUG ]
[DEBUG ] 23 GMXMMPBSA_REC_GMXMMPBSA_LIG: 4052 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_MOL (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f md-nopbc.xtc -s md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda
[DEBUG ] Executable: /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /root/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /root/PBSA/╫╘╩╔/Beclin1
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md-nopbc.xtc -s md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Group 0 ( System) has 63006 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3972 elements
[DEBUG ] Group 2 ( Protein-H) has 1997 elements
[DEBUG ] Group 3 ( C-alpha) has 235 elements
[DEBUG ] Group 4 ( Backbone) has 705 elements
[DEBUG ] Group 5 ( MainChain) has 939 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1166 elements
[DEBUG ] Group 7 ( MainChain+H) has 1158 elements
[DEBUG ] Group 8 ( SideChain) has 2814 elements
[DEBUG ] Group 9 ( SideChain-H) has 1058 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3972 elements
[DEBUG ] Group 11 ( non-Protein) has 59034 elements
[DEBUG ] Group 12 ( Other) has 80 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 80 elements
[DEBUG ] Group 14 ( CL) has 4 elements
[DEBUG ] Group 15 ( Water) has 58950 elements
[DEBUG ] Group 16 ( SOL) has 58950 elements
[DEBUG ] Group 17 ( non-Water) has 4056 elements
[DEBUG ] Group 18 ( Ion) has 4 elements
[DEBUG ] Group 19 ( MOL) has 80 elements
[DEBUG ] Group 20 ( CL) has 4 elements
[DEBUG ] Group 21 ( Water_and_ions) has 58954 elements
[DEBUG ] Group 22 ( Protein_MOL) has 4052 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4052 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md-nopbc.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 10.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Louis Pasteur's theory of germs is ridiculous fiction." (Pierre Pachet, Professor of Physiology at Toulouse, 1872)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 23: '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 Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo -e "1"| /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f md-nopbc.xtc -s md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda
[DEBUG ] Executable: /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /root/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /root/PBSA/╫╘╩╔/Beclin1
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md-nopbc.xtc -s md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Group 0 ( System) has 63006 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3972 elements
[DEBUG ] Group 2 ( Protein-H) has 1997 elements
[DEBUG ] Group 3 ( C-alpha) has 235 elements
[DEBUG ] Group 4 ( Backbone) has 705 elements
[DEBUG ] Group 5 ( MainChain) has 939 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1166 elements
[DEBUG ] Group 7 ( MainChain+H) has 1158 elements
[DEBUG ] Group 8 ( SideChain) has 2814 elements
[DEBUG ] Group 9 ( SideChain-H) has 1058 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3972 elements
[DEBUG ] Group 11 ( non-Protein) has 59034 elements
[DEBUG ] Group 12 ( Other) has 80 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 80 elements
[DEBUG ] Group 14 ( CL) has 4 elements
[DEBUG ] Group 15 ( Water) has 58950 elements
[DEBUG ] Group 16 ( SOL) has 58950 elements
[DEBUG ] Group 17 ( non-Water) has 4056 elements
[DEBUG ] Group 18 ( Ion) has 4 elements
[DEBUG ] Group 19 ( MOL) has 80 elements
[DEBUG ] Group 20 ( CL) has 4 elements
[DEBUG ] Group 21 ( Water_and_ions) has 58954 elements
[DEBUG ] Group 22 ( Protein_MOL) has 4052 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4052 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md-nopbc.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 10.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ]
[DEBUG ] GROMACS reminds you: "I had a polynomial once. My doctor removed it." (Michael Grant)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 1: '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 MOL (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo -e "13"| /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f md-nopbc.xtc -s md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda
[DEBUG ] Executable: /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /root/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /root/PBSA/╫╘╩╔/Beclin1
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md-nopbc.xtc -s md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Group 0 ( System) has 63006 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3972 elements
[DEBUG ] Group 2 ( Protein-H) has 1997 elements
[DEBUG ] Group 3 ( C-alpha) has 235 elements
[DEBUG ] Group 4 ( Backbone) has 705 elements
[DEBUG ] Group 5 ( MainChain) has 939 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1166 elements
[DEBUG ] Group 7 ( MainChain+H) has 1158 elements
[DEBUG ] Group 8 ( SideChain) has 2814 elements
[DEBUG ] Group 9 ( SideChain-H) has 1058 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3972 elements
[DEBUG ] Group 11 ( non-Protein) has 59034 elements
[DEBUG ] Group 12 ( Other) has 80 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 80 elements
[DEBUG ] Group 14 ( CL) has 4 elements
[DEBUG ] Group 15 ( Water) has 58950 elements
[DEBUG ] Group 16 ( SOL) has 58950 elements
[DEBUG ] Group 17 ( non-Water) has 4056 elements
[DEBUG ] Group 18 ( Ion) has 4 elements
[DEBUG ] Group 19 ( MOL) has 80 elements
[DEBUG ] Group 20 ( CL) has 4 elements
[DEBUG ] Group 21 ( Water_and_ions) has 58954 elements
[DEBUG ] Group 22 ( Protein_MOL) has 4052 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4052 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md-nopbc.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 10.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ]
[DEBUG ] GROMACS reminds you: "We're Gonna Hit You Harder" (Scoter)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 13: 'GMXMMPBSA_LIG'
[INFO ] Checking the structures consistency...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
[INFO ] Detected CHARMM 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 ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis...
[INFO ] Selected 13 residues:
R:A:PRO:11 R:A:PHE:12 R:A:GLU:13 R:A:TYR:14 R:A:ARG:15 R:A:LYS:16 R:A:LYS:17 R:A:GLU:18 R:A:LYS:156 R:A:ALA:157
R:A:ARG:158 R:A:LYS:235 L:B:MOL:236

[INFO ] Cleaning normal complex trajectories...
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f md-nopbc.xtc -s md.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG ] :-) GROMACS - gmx trjconv, 2021.3-bioconda (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Andrey Alekseenko Emile Apol Rossen Apostolov
[DEBUG ] Paul Bauer Herman J.C. Berendsen Par Bjelkmar
[DEBUG ] Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra
[DEBUG ] Gilles Gouaillardet Alan Gray Gerrit Groenhof
[DEBUG ] Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan
[DEBUG ] Dimitrios Karkoulis Peter Kasson Jiri Kraus
[DEBUG ] Carsten Kutzner Per Larsson Justin A. Lemkul
[DEBUG ] Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola
[DEBUG ] Szilard Pall Sander Pronk Roland Schulz
[DEBUG ] Michael Shirts Alexey Shvetsov Alfons Sijbers
[DEBUG ] Peter Tieleman Jon Vincent Teemu Virolainen
[DEBUG ] Christian Wennberg Maarten Wolf Artem Zhmurov
[DEBUG ] and the project leaders:
[DEBUG ] Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
[DEBUG ]
[DEBUG ] Copyright (c) 1991-2000, University of Groningen, The Netherlands.
[DEBUG ] Copyright (c) 2001-2019, The GROMACS development team at
[DEBUG ] Uppsala University, Stockholm University and
[DEBUG ] the Royal Institute of Technology, Sweden.
[DEBUG ] check out http://www.gromacs.org for more information.
[DEBUG ]
[DEBUG ] GROMACS is free software; you can redistribute it and/or modify it
[DEBUG ] under the terms of the GNU Lesser General Public License
[DEBUG ] as published by the Free Software Foundation; either version 2.1
[DEBUG ] of the License, or (at your option) any later version.
[DEBUG ]
[DEBUG ] GROMACS: gmx trjconv, version 2021.3-bioconda
[DEBUG ] Executable: /root/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /root/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /root/PBSA/╫╘╩╔/Beclin1
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md-nopbc.xtc -s md.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG ]
[DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Reading file md.tpr, VERSION 2020.6-MODIFIED (single precision)
[DEBUG ] Group 0 ( System) has 63006 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3972 elements
[DEBUG ] Group 2 ( Protein-H) has 1997 elements
[DEBUG ] Group 3 ( C-alpha) has 235 elements
[DEBUG ] Group 4 ( Backbone) has 705 elements
[DEBUG ] Group 5 ( MainChain) has 939 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1166 elements
[DEBUG ] Group 7 ( MainChain+H) has 1158 elements
[DEBUG ] Group 8 ( SideChain) has 2814 elements
[DEBUG ] Group 9 ( SideChain-H) has 1058 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3972 elements
[DEBUG ] Group 11 ( non-Protein) has 59034 elements
[DEBUG ] Group 12 ( Other) has 80 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 80 elements
[DEBUG ] Group 14 ( CL) has 4 elements
[DEBUG ] Group 15 ( Water) has 58950 elements
[DEBUG ] Group 16 ( SOL) has 58950 elements
[DEBUG ] Group 17 ( non-Water) has 4056 elements
[DEBUG ] Group 18 ( Ion) has 4 elements
[DEBUG ] Group 19 ( MOL) has 80 elements
[DEBUG ] Group 20 ( CL) has 4 elements
[DEBUG ] Group 21 ( Water_and_ions) has 58954 elements
[DEBUG ] Group 22 ( Protein_MOL) has 4052 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4052 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md-nopbc.xtc is 0.001 (nm)
[DEBUG ] Using output precision of 0.001 (nm)
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Don't waste pure thoughts on dirty enzymes." (Efraim Racker)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 23: '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 ] 101 frames were processed by cpptraj for use in calculation.
[INFO ] Starting calculations in 8 CPUs...
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.
[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
[INFO ] calculating receptor contribution...
[INFO ] calculating ligand contribution...
[INFO ] Beginning PB calculations with /root/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...

Operating system

Linux, Ubuntu

gmx_MMPBSA Version

gmx_MMPBSA v1.6.3 based on MMPBSA version 16.0 and AmberTools 20

Python version

Python 3.9.15

Installation

pip

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