I am getting the following error after all the calculations are done. There seems to be some issue with the parsing the result. Is there any way to resume from where the process ended as the calculations are already done?
Terminal output
mpirun -n 10 gmx_MMPBSA -O -i ../mmpbsa.in -cs ../Analysis/Protein2.tpr -ct ../step5_production_250ns.xtc -ci ../pbsa-index.ndx -cg 15 16 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO ] Starting gmx_MMPBSA v1.6.1
[INFO ] Command-line
mpirun -np 10 gmx_MMPBSA -O -i ../mmpbsa.in -cs ../Analysis/Protein2.tpr -ct ../step5_production_250ns.xtc -ci ../pbsa-index.ndx -cg 15 16 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[INFO ] Checking ../mmpbsa.in input file...
[INFO ] Checking ../mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/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 chB_chA_UNL (15_16) 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 chB (15) 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 chA_UNL (16) 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 (4 Å) between receptor and ligand for decomposition analysis...
[INFO ] Selected 32 residues:
L:A:MET:40 L:A:HSD:44 L:A:VAL:45 L:A:SER:46 L:A:LEU:47 L:A:GLU:124 L:A:GLN:125 L:A:LEU:126 L:A:GLY:127 L:A:ILE:128
L:A:PRO:129 L:A:ASP:232 L:A:VAL:233 L:A:PRO:234 L:A:TYR:250 L:A:LEU:251 L:A:ALA:252 L:A:PRO:253 L:A:LYS:254 L:A:ILE:255
R:B:GLY:1069 R:B:SER:1070 R:B:ASP:1071 R:B:ILE:1072 R:B:THR:1073 R:B:ARG:1074 R:B:PHE:1075
R:B:LEU:1076 R:B:VAL:1077 R:B:LYS:1078 R:B:LYS:1079 L:C:UNL:1080
[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 ] 501 frames were processed by cpptraj for use in calculation.
[INFO ] Starting calculations in 10 CPUs...
[WARNING] PB/RISM/NMODE will be calculated with multiple threads, make sure you have enough RAM.
tets
[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
100%|##########| 501/501 [elapsed: 21:09 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|##########| 501/501 [elapsed: 00:37 remaining: 00:00]
[INFO ] calculating ligand contribution...
100%|##########| 501/501 [elapsed: 22:34 remaining: 00:00]
[INFO ] Beginning PB calculations with /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
100%|##########| 501/501 [elapsed: 2:18:17 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|##########| 501/501 [elapsed: 05:09 remaining: 00:00]
[INFO ] calculating ligand contribution...
26%|##5 | 130/501 [elapsed: 25:35 remaining: 1:15:02]
100%|##########| 501/501 [elapsed: 2:20:58 remaining: 00:00]
[INFO ] Parsing results to output files...
File "/home/aka/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
sys.exit(gmxmmpbsa())
File "/home/aka/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 109, in gmxmmpbsa
app.parse_output_files()
File "/home/aka/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1271, in parse_output_files
self._get_decomp()
File "/home/aka/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1426, in _get_decomp
self.calc_types.decomp_normal[key]['complex'].parse_from_file(self.pre + basename[i] % 'complex',
File "/home/aka/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 1371, in parse_from_file
self._read()
File "/home/aka/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 1399, in _read
self._get_decomp_energies(output_file)
File "/home/aka/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/amber_outputs.py", line 1410, in _get_decomp_energies
internal = float(line[11:20])
ValueError: could not convert string to float: '*********'
Error occurred on rank 0.
Exiting. All files have been retained.
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
gmx_MMPBSA.log
[INFO ] Starting gmx_MMPBSA v1.6.1
[DEBUG ] WDIR : /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA
[DEBUG ] AMBERHOME : /home/aka/miniconda3/envs/gmxMMPBSA
[DEBUG ] PYTHON EXE : /home/aka/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG ] PYTHON VERSION: 3.9.7 | packaged by conda-forge | (default, Sep 2 2021, 17:58:34) [GCC 9.4.0]
[DEBUG ] MPI : /home/aka/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG ] ParmEd : 3.4.1
[DEBUG ] OS PLATFORM : Linux-5.19.0-50-generic-x86_64-with-glibc2.35
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #50-Ubuntu SMP PREEMPT_DYNAMIC Mon Jul 10 18:24:29 UTC 2023
[DEBUG ] OS PROCESSOR : x86_64
[DEBUG ] |Input file:
[DEBUG ] |--------------------------------------------------------------
[DEBUG ] |Input file generated by gmx_MMPBSA (v1.5.6)
[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 = "protein-protein" # System name
[DEBUG ] | startframe = 1500 # First frame to analyze
[DEBUG ] | endframe = 2000 # 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 ] | 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 ] | 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 = 2 # 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 = 0.15 # 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 = 2 # Control energy terms are printed to the output
[DEBUG ] | print_res = "within 4" # 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 /home/aka/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /usr/local/gromacs/bin/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...
[DEBUG ] Running command: echo -e "name 15 GMXMMPBSA_REC\n name 16 GMXMMPBSA_LIG\n 15 | 16\n q\n" | /usr/local/gromacs/bin/bin/gmx make_ndx -n ../index-pbsa.ndx -o _GMXMMPBSA_COM_index.ndx -f ../Analysis/Protein3.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2020.6 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6
[DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx
[DEBUG ] Data prefix: /usr/local/gromacs/bin
[DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n ../index-pbsa.ndx -o _GMXMMPBSA_COM_index.ndx -f ../Analysis/Protein3.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Look at these, my work-strong arms" (P.J. Harvey)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 4170 atoms
[DEBUG ] 1 Protein : 4116 atoms
[DEBUG ] 2 Protein-H : 2047 atoms
[DEBUG ] 3 C-alpha : 266 atoms
[DEBUG ] 4 Backbone : 798 atoms
[DEBUG ] 5 MainChain : 1062 atoms
[DEBUG ] 6 MainChain+Cb : 1314 atoms
[DEBUG ] 7 MainChain+H : 1319 atoms
[DEBUG ] 8 SideChain : 2797 atoms
[DEBUG ] 9 SideChain-H : 985 atoms
[DEBUG ] 10 Prot-Masses : 4116 atoms
[DEBUG ] 11 non-Protein : 54 atoms
[DEBUG ] 12 Other : 54 atoms
[DEBUG ] 13 UNL : 54 atoms
[DEBUG ] 14 chA : 3937 atoms
[DEBUG ] 15 chB : 179 atoms
[DEBUG ] 16 chA_UNL : 3991 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 15 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 16 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 179 3991 -> 4170
[DEBUG ]
[DEBUG ] 17 GMXMMPBSA_REC_GMXMMPBSA_LIG: 4170 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group chB_chA_UNL (15_16) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6
[DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx
[DEBUG ] Data prefix: /usr/local/gromacs/bin
[DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Group 0 ( System) has 4170 elements
[DEBUG ] Group 1 ( Protein) has 4116 elements
[DEBUG ] Group 2 ( Protein-H) has 2047 elements
[DEBUG ] Group 3 ( C-alpha) has 266 elements
[DEBUG ] Group 4 ( Backbone) has 798 elements
[DEBUG ] Group 5 ( MainChain) has 1062 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements
[DEBUG ] Group 7 ( MainChain+H) has 1319 elements
[DEBUG ] Group 8 ( SideChain) has 2797 elements
[DEBUG ] Group 9 ( SideChain-H) has 985 elements
[DEBUG ] Group 10 ( Prot-Masses) has 4116 elements
[DEBUG ] Group 11 ( non-Protein) has 54 elements
[DEBUG ] Group 12 ( Other) has 54 elements
[DEBUG ] Group 13 ( UNL) has 54 elements
[DEBUG ] Group 14 ( chA) has 3937 elements
[DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements
[DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements
[DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps
[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 17: '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 chB (15) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo -e "15"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6
[DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx
[DEBUG ] Data prefix: /usr/local/gromacs/bin
[DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Group 0 ( System) has 4170 elements
[DEBUG ] Group 1 ( Protein) has 4116 elements
[DEBUG ] Group 2 ( Protein-H) has 2047 elements
[DEBUG ] Group 3 ( C-alpha) has 266 elements
[DEBUG ] Group 4 ( Backbone) has 798 elements
[DEBUG ] Group 5 ( MainChain) has 1062 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements
[DEBUG ] Group 7 ( MainChain+H) has 1319 elements
[DEBUG ] Group 8 ( SideChain) has 2797 elements
[DEBUG ] Group 9 ( SideChain-H) has 985 elements
[DEBUG ] Group 10 ( Prot-Masses) has 4116 elements
[DEBUG ] Group 11 ( non-Protein) has 54 elements
[DEBUG ] Group 12 ( Other) has 54 elements
[DEBUG ] Group 13 ( UNL) has 54 elements
[DEBUG ] Group 14 ( chA) has 3937 elements
[DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements
[DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements
[DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps
[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 15: '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 chA_UNL (16) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo -e "16"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6
[DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx
[DEBUG ] Data prefix: /usr/local/gromacs/bin
[DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Group 0 ( System) has 4170 elements
[DEBUG ] Group 1 ( Protein) has 4116 elements
[DEBUG ] Group 2 ( Protein-H) has 2047 elements
[DEBUG ] Group 3 ( C-alpha) has 266 elements
[DEBUG ] Group 4 ( Backbone) has 798 elements
[DEBUG ] Group 5 ( MainChain) has 1062 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements
[DEBUG ] Group 7 ( MainChain+H) has 1319 elements
[DEBUG ] Group 8 ( SideChain) has 2797 elements
[DEBUG ] Group 9 ( SideChain-H) has 985 elements
[DEBUG ] Group 10 ( Prot-Masses) has 4116 elements
[DEBUG ] Group 11 ( non-Protein) has 54 elements
[DEBUG ] Group 12 ( Other) has 54 elements
[DEBUG ] Group 13 ( UNL) has 54 elements
[DEBUG ] Group 14 ( chA) has 3937 elements
[DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements
[DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements
[DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Water is just water" (Berk Hess)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 16: '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 (4 Å) between receptor and ligand for decomposition analysis...
[INFO ] Selected 31 residues:
L:A:MET:40 L:A:HSD:44 L:A:VAL:45 L:A:SER:46 L:A:LEU:47 L:A:GLU:124 L:A:GLN:125 L:A:LEU:126 L:A:GLY:127 L:A:ILE:128
L:A:PRO:129 L:A:ALA:208 L:A:PRO:234 L:A:TYR:250 L:A:LEU:251 L:A:ALA:252 L:A:PRO:253 L:A:LYS:254 L:A:ILE:255 R:B:GLY:1069
R:B:SER:1070 R:B:ASP:1071 R:B:ILE:1072 R:B:THR:1073 R:B:ARG:1074 R:B:ALA:1075 R:B:LEU:1076
R:B:VAL:1077 R:B:LYS:1078 R:B:LYS:1079 L:C:UNL:1080
[INFO ] Cleaning normal complex trajectories...
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-:
[DEBUG ]
[DEBUG ] GROMACS is written by:
[DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen
[DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis
[DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6
[DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx
[DEBUG ] Data prefix: /usr/local/gromacs/bin
[DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.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 ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision)
[DEBUG ] Group 0 ( System) has 4170 elements
[DEBUG ] Group 1 ( Protein) has 4116 elements
[DEBUG ] Group 2 ( Protein-H) has 2047 elements
[DEBUG ] Group 3 ( C-alpha) has 266 elements
[DEBUG ] Group 4 ( Backbone) has 798 elements
[DEBUG ] Group 5 ( MainChain) has 1062 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements
[DEBUG ] Group 7 ( MainChain+H) has 1319 elements
[DEBUG ] Group 8 ( SideChain) has 2797 elements
[DEBUG ] Group 9 ( SideChain-H) has 985 elements
[DEBUG ] Group 10 ( Prot-Masses) has 4116 elements
[DEBUG ] Group 11 ( non-Protein) has 54 elements
[DEBUG ] Group 12 ( Other) has 54 elements
[DEBUG ] Group 13 ( UNL) has 54 elements
[DEBUG ] Group 14 ( chA) has 3937 elements
[DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements
[DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements
[DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm)
[DEBUG ] Using output precision of 0.001 (nm)
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 17: '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 ] 501 frames were processed by cpptraj for use in calculation.
[INFO ] Starting calculations in 6 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 /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
[INFO ] calculating receptor contribution...
[INFO ] calculating ligand contribution...
[INFO ] Beginning PB calculations with /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] calculating complex contribution...
[INFO ] calculating receptor contribution...
[INFO ] calculating ligand contribution...
[INFO ] Parsing results to output files...
avinashkarkada
commented
1 year ago
Bug summary
I am getting the following error after all the calculations are done. There seems to be some issue with the parsing the result. Is there any way to resume from where the process ended as the calculations are already done?
Terminal output
gmx_MMPBSA.log
[INFO ] Starting gmx_MMPBSA v1.6.1 [DEBUG ] WDIR : /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA [DEBUG ] AMBERHOME : /home/aka/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /home/aka/miniconda3/envs/gmxMMPBSA/bin/python [DEBUG ] PYTHON VERSION: 3.9.7 | packaged by conda-forge | (default, Sep 2 2021, 17:58:34) [GCC 9.4.0] [DEBUG ] MPI : /home/aka/miniconda3/envs/gmxMMPBSA/bin/mpirun [DEBUG ] ParmEd : 3.4.1 [DEBUG ] OS PLATFORM : Linux-5.19.0-50-generic-x86_64-with-glibc2.35 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #50-Ubuntu SMP PREEMPT_DYNAMIC Mon Jul 10 18:24:29 UTC 2023 [DEBUG ] OS PROCESSOR : x86_64
[INFO ] Command-line mpirun -np 6 gmx_MMPBSA -O -i ../mmpbsa.in -cs ../Analysis/Protein3.tpr -ct ../step5_production_250ns.xtc -ci ../index-pbsa.ndx -cg 15 16 -cp ../topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[DEBUG ] |Input file: [DEBUG ] |-------------------------------------------------------------- [DEBUG ] |Input file generated by gmx_MMPBSA (v1.5.6) [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 = "protein-protein" # System name [DEBUG ] | startframe = 1500 # First frame to analyze [DEBUG ] | endframe = 2000 # 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 ] | 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 ] | 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 = 2 # 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 = 0.15 # 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 = 2 # Control energy terms are printed to the output [DEBUG ] | print_res = "within 4" # 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 /home/aka/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /usr/local/gromacs/bin/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... [DEBUG ] Running command: echo -e "name 15 GMXMMPBSA_REC\n name 16 GMXMMPBSA_LIG\n 15 | 16\n q\n" | /usr/local/gromacs/bin/bin/gmx make_ndx -n ../index-pbsa.ndx -o _GMXMMPBSA_COM_index.ndx -f ../Analysis/Protein3.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2020.6 (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen [DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis [DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6 [DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx [DEBUG ] Data prefix: /usr/local/gromacs/bin [DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n ../index-pbsa.ndx -o _GMXMMPBSA_COM_index.ndx -f ../Analysis/Protein3.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "Look at these, my work-strong arms" (P.J. Harvey) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 System : 4170 atoms [DEBUG ] 1 Protein : 4116 atoms [DEBUG ] 2 Protein-H : 2047 atoms [DEBUG ] 3 C-alpha : 266 atoms [DEBUG ] 4 Backbone : 798 atoms [DEBUG ] 5 MainChain : 1062 atoms [DEBUG ] 6 MainChain+Cb : 1314 atoms [DEBUG ] 7 MainChain+H : 1319 atoms [DEBUG ] 8 SideChain : 2797 atoms [DEBUG ] 9 SideChain-H : 985 atoms [DEBUG ] 10 Prot-Masses : 4116 atoms [DEBUG ] 11 non-Protein : 54 atoms [DEBUG ] 12 Other : 54 atoms [DEBUG ] 13 UNL : 54 atoms [DEBUG ] 14 chA : 3937 atoms [DEBUG ] 15 chB : 179 atoms [DEBUG ] 16 chA_UNL : 3991 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 15 'GMXMMPBSA_REC' [DEBUG ] Copied index group 16 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 179 3991 -> 4170 [DEBUG ] [DEBUG ] 17 GMXMMPBSA_REC_GMXMMPBSA_LIG: 4170 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group chB_chA_UNL (15_16) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen [DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis [DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6 [DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx [DEBUG ] Data prefix: /usr/local/gromacs/bin [DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Group 0 ( System) has 4170 elements [DEBUG ] Group 1 ( Protein) has 4116 elements [DEBUG ] Group 2 ( Protein-H) has 2047 elements [DEBUG ] Group 3 ( C-alpha) has 266 elements [DEBUG ] Group 4 ( Backbone) has 798 elements [DEBUG ] Group 5 ( MainChain) has 1062 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements [DEBUG ] Group 7 ( MainChain+H) has 1319 elements [DEBUG ] Group 8 ( SideChain) has 2797 elements [DEBUG ] Group 9 ( SideChain-H) has 985 elements [DEBUG ] Group 10 ( Prot-Masses) has 4116 elements [DEBUG ] Group 11 ( non-Protein) has 54 elements [DEBUG ] Group 12 ( Other) has 54 elements [DEBUG ] Group 13 ( UNL) has 54 elements [DEBUG ] Group 14 ( chA) has 3937 elements [DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements [DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements [DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps [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 17: '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 chB (15) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo -e "15"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen [DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis [DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6 [DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx [DEBUG ] Data prefix: /usr/local/gromacs/bin [DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Group 0 ( System) has 4170 elements [DEBUG ] Group 1 ( Protein) has 4116 elements [DEBUG ] Group 2 ( Protein-H) has 2047 elements [DEBUG ] Group 3 ( C-alpha) has 266 elements [DEBUG ] Group 4 ( Backbone) has 798 elements [DEBUG ] Group 5 ( MainChain) has 1062 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements [DEBUG ] Group 7 ( MainChain+H) has 1319 elements [DEBUG ] Group 8 ( SideChain) has 2797 elements [DEBUG ] Group 9 ( SideChain-H) has 985 elements [DEBUG ] Group 10 ( Prot-Masses) has 4116 elements [DEBUG ] Group 11 ( non-Protein) has 54 elements [DEBUG ] Group 12 ( Other) has 54 elements [DEBUG ] Group 13 ( UNL) has 54 elements [DEBUG ] Group 14 ( chA) has 3937 elements [DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements [DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements [DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps [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 15: '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 chA_UNL (16) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo -e "16"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen [DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis [DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6 [DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx [DEBUG ] Data prefix: /usr/local/gromacs/bin [DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Group 0 ( System) has 4170 elements [DEBUG ] Group 1 ( Protein) has 4116 elements [DEBUG ] Group 2 ( Protein-H) has 2047 elements [DEBUG ] Group 3 ( C-alpha) has 266 elements [DEBUG ] Group 4 ( Backbone) has 798 elements [DEBUG ] Group 5 ( MainChain) has 1062 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements [DEBUG ] Group 7 ( MainChain+H) has 1319 elements [DEBUG ] Group 8 ( SideChain) has 2797 elements [DEBUG ] Group 9 ( SideChain-H) has 985 elements [DEBUG ] Group 10 ( Prot-Masses) has 4116 elements [DEBUG ] Group 11 ( non-Protein) has 54 elements [DEBUG ] Group 12 ( Other) has 54 elements [DEBUG ] Group 13 ( UNL) has 54 elements [DEBUG ] Group 14 ( chA) has 3937 elements [DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements [DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements [DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 100.000
Reading frame 0 time 0.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] [DEBUG ] GROMACS reminds you: "Water is just water" (Berk Hess) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 16: '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 (4 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 31 residues: L:A:MET:40 L:A:HSD:44 L:A:VAL:45 L:A:SER:46 L:A:LEU:47 L:A:GLU:124 L:A:GLN:125 L:A:LEU:126 L:A:GLY:127 L:A:ILE:128 L:A:PRO:129 L:A:ALA:208 L:A:PRO:234 L:A:TYR:250 L:A:LEU:251 L:A:ALA:252 L:A:PRO:253 L:A:LYS:254 L:A:ILE:255 R:B:GLY:1069 R:B:SER:1070 R:B:ASP:1071 R:B:ILE:1072 R:B:THR:1073 R:B:ARG:1074 R:B:ALA:1075 R:B:LEU:1076 R:B:VAL:1077 R:B:LYS:1078 R:B:LYS:1079 L:C:UNL:1080
[INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /usr/local/gromacs/bin/bin/gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2020.6 (-: [DEBUG ] [DEBUG ] GROMACS is written by: [DEBUG ] Emile Apol Rossen Apostolov Paul Bauer Herman J.C. Berendsen [DEBUG ] Par Bjelkmar Christian Blau Viacheslav Bolnykh Kevin Boyd
[DEBUG ] Aldert van Buuren Rudi van Drunen Anton Feenstra Alan Gray
[DEBUG ] Gerrit Groenhof Anca Hamuraru Vincent Hindriksen M. Eric Irrgang
[DEBUG ] Aleksei Iupinov Christoph Junghans Joe Jordan Dimitrios Karkoulis [DEBUG ] Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
[DEBUG ] Justin A. Lemkul Viveca Lindahl Magnus Lundborg Erik Marklund
[DEBUG ] Pascal Merz Pieter Meulenhoff Teemu Murtola Szilard Pall
[DEBUG ] Sander Pronk Roland Schulz Michael Shirts Alexey Shvetsov
[DEBUG ] Alfons Sijbers 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 2020.6 [DEBUG ] Executable: /usr/local/gromacs/bin/bin/gmx [DEBUG ] Data prefix: /usr/local/gromacs/bin [DEBUG ] Working dir: /media/aka/OS/Users/alekh/Desktop/PCNA/RPB1/SIM/T1/T1-SIM/3_NA_F4A-LIG/gromacs/P-P_PGBSA [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../step5_production_250ns.xtc -s ../Analysis/Protein3.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 ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Reading file ../Analysis/Protein3.tpr, VERSION 2020.6 (single precision) [DEBUG ] Group 0 ( System) has 4170 elements [DEBUG ] Group 1 ( Protein) has 4116 elements [DEBUG ] Group 2 ( Protein-H) has 2047 elements [DEBUG ] Group 3 ( C-alpha) has 266 elements [DEBUG ] Group 4 ( Backbone) has 798 elements [DEBUG ] Group 5 ( MainChain) has 1062 elements [DEBUG ] Group 6 ( MainChain+Cb) has 1314 elements [DEBUG ] Group 7 ( MainChain+H) has 1319 elements [DEBUG ] Group 8 ( SideChain) has 2797 elements [DEBUG ] Group 9 ( SideChain-H) has 985 elements [DEBUG ] Group 10 ( Prot-Masses) has 4116 elements [DEBUG ] Group 11 ( non-Protein) has 54 elements [DEBUG ] Group 12 ( Other) has 54 elements [DEBUG ] Group 13 ( UNL) has 54 elements [DEBUG ] Group 14 ( chA) has 3937 elements [DEBUG ] Group 15 ( GMXMMPBSA_REC) has 179 elements [DEBUG ] Group 16 ( GMXMMPBSA_LIG) has 3991 elements [DEBUG ] Group 17 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 4170 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../step5_production_250ns.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "You're like them scientists on TV explaining black holes. More you talk, less I get" (Jess Walter) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 17: '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 ] 501 frames were processed by cpptraj for use in calculation. [INFO ] Starting calculations in 6 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 /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] calculating ligand contribution... [INFO ] Beginning PB calculations with /home/aka/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] calculating ligand contribution... [INFO ] Parsing results to output files...
Operating system
Ununtu
gmx_MMPBSA Version
v1.6.1
Python version
Python 3.9.7
Installation
None