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Valdes-Tresanco-MS / gmx_MMPBSA

gmx_MMPBSA is a new tool based on AMBER's MMPBSA.py aiming to perform end-state free energy calculations with GROMACS files.
https://valdes-tresanco-ms.github.io/gmx_MMPBSA/
GNU General Public License v3.0
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[Bug-gmx_MMPBSA]: KeyError:"ie" #279

Closed WXYWD closed 2 years ago

WXYWD commented 2 years ago

Bug summary

When I was calculating my protein-ligand complex, an error occurred during the processs

Terminal output

File "/home/yxp212121/yxp/amber20/miniconda/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/yxp212121/yxp/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 112, in gmxmmpbsa
    app.parse_output_files()
  File "/home/yxp212121/yxp/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1088, in parse_output_files
    self.get_iec2entropy(from_calc)
  File "/home/yxp212121/yxp/amber20/miniconda/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 1127, in get_iec2entropy
    self.calc_types.mutant['ie'], self.calc_types.normal['ie'])
KeyError: 'ie'
Error occurred on rank 0.
Exiting. All files have been retained.

gmx_MMPBSA.log

gmx_MMPBSA.log [INFO ] Starting gmx_MMPBSA v1.5.6 [DEBUG ] WDIR : /home/yxp212121/yxp/MMPBSA/Ks5A74R1jxmnCB-100ns-dt100ps-group0 [DEBUG ] AMBERHOME : /home/yxp212121/yxp/amber20 [DEBUG ] PYTHON EXE : /home/yxp212121/yxp/amber20/miniconda/bin/python [DEBUG ] PYTHON VERSION: 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] [DEBUG ] MPI : /home/yxp212121/yxp/openmpi/bin/mpirun [DEBUG ] ParmEd : 3.4.3+10.ga195c7ec [DEBUG ] OS PLATFORM : Linux-4.18.0-348.7.1.el8_5.x86_64-x86_64-with-glibc2.28 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #1 SMP Wed Dec 22 13:25:12 UTC 2021 [DEBUG ] OS PROCESSOR : x86_64 [INFO ] Command-line mpirun -np 2 gmx_MMPBSA MPI -O -i mmpbsa.in -cs md.tpr -ci index.ndx -cg 1 13 -ct K4R1CB.xtc -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -do FINAL_DECOMP_MMPBSA.dat -deo FINAL_DECOMP_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 = "K4R1CB" # System name [DEBUG ] | startframe = 1 # First frame to analyze [DEBUG ] | endframe = 1000 # Last frame to analyze [DEBUG ] | interval = 1 # Number of frames between adjacent frames analyzed [DEBUG ] | forcefields = "leaprc.protein.ff14SB,leaprc.GLYCAM_06j-1" # 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 = 323.15 # Temperature [DEBUG ] | qh_entropy = 0 # Do quasi-harmonic calculation [DEBUG ] | interaction_entropy = 1 # 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) 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 = 0.0 # 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 ] |# Alanine scanning namelist variables [DEBUG ] |&alanine_scanning [DEBUG ] | mutant_res = "A/253" # Which residue will be mutated [DEBUG ] | mutant = "ALA" # Defines if Alanine or Glycine scanning will be performed [DEBUG ] | mutant_only = 0 # Only compute mutant energies [DEBUG ] | cas_intdiel = 0 # Change the intdiel value based on which aa is mutated [DEBUG ] | intdiel_nonpolar = 1 # intdiel for nonpolar residues [DEBUG ] | intdiel_polar = 3 # intdiel for polar residues [DEBUG ] | intdiel_positive = 5 # intdiel for positive charged residues [DEBUG ] | intdiel_negative = 5 # intdiel for negative charged residues [DEBUG ] |/ [DEBUG ] | [DEBUG ] |# Decomposition namelist variables [DEBUG ] |&decomposition [DEBUG ] | idecomp = 2 # Which type of decomposition analysis to do [DEBUG ] | dec_verbose = 3 # 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 /home/yxp212121/yxp/amber20/bin/cpptraj [INFO ] tleap found! Using /home/yxp212121/yxp/amber20/bin/tleap [INFO ] parmchk2 found! Using /home/yxp212121/yxp/amber20/bin/parmchk2 [INFO ] sander found! Using /home/yxp212121/yxp/amber20/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/yxp212121/yxp/gmx2019/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 name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n | /home/yxp212121/yxp/gmx2019/bin/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx make_ndx, 2019.6 (-: [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 [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) 2001-2018, 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 2019.6 [DEBUG ] Executable: /home/yxp212121/yxp/gmx2019/bin/gmx [DEBUG ] Data prefix: /home/yxp212121/yxp/gmx2019 [DEBUG ] Working dir: /home/yxp212121/yxp/MMPBSA/Ks5A74R1jxmnCB-100ns-dt100ps-group0 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "With four parameters I can fit an elephant, and with five I can make him wiggle his trunk." (John von Neumann) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] Counted atom numbers up to 73469 in index file [DEBUG ] [DEBUG ] 0 System : 73469 atoms [DEBUG ] 1 Protein : 7294 atoms [DEBUG ] 2 Protein-H : 3716 atoms [DEBUG ] 3 C-alpha : 451 atoms [DEBUG ] 4 Backbone : 1353 atoms [DEBUG ] 5 MainChain : 1805 atoms [DEBUG ] 6 MainChain+Cb : 2220 atoms [DEBUG ] 7 MainChain+H : 2238 atoms [DEBUG ] 8 SideChain : 5056 atoms [DEBUG ] 9 SideChain-H : 1911 atoms [DEBUG ] 10 Prot-Masses : 7294 atoms [DEBUG ] 11 non-Protein : 66175 atoms [DEBUG ] 12 Other : 45 atoms [DEBUG ] 13 CBI : 45 atoms [DEBUG ] 14 K : 55 atoms [DEBUG ] 15 CL : 45 atoms [DEBUG ] 16 Water : 66030 atoms [DEBUG ] 17 SOL : 66030 atoms [DEBUG ] 18 non-Water : 7439 atoms [DEBUG ] 19 Ion : 100 atoms [DEBUG ] 20 CBI : 45 atoms [DEBUG ] 21 K : 55 atoms [DEBUG ] 22 CL : 45 atoms [DEBUG ] 23 Water_and_ions : 66130 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: 7294 45 -> 7339 [DEBUG ] [DEBUG ] 24 GMXMMPBSA_REC_GMXMMPBSA_LIG: 7339 atoms [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group 1_13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /home/yxp212121/yxp/gmx2019/bin/gmx trjconv -f K4R1CB.xtc -s md.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2019.6 (-: [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 [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) 2001-2018, 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 2019.6 [DEBUG ] Executable: /home/yxp212121/yxp/gmx2019/bin/gmx [DEBUG ] Data prefix: /home/yxp212121/yxp/gmx2019 [DEBUG ] Working dir: /home/yxp212121/yxp/MMPBSA/Ks5A74R1jxmnCB-100ns-dt100ps-group0 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f K4R1CB.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 2019.6 (single precision) [DEBUG ] Reading file md.tpr, VERSION 2019.6 (single precision) [DEBUG ] Group 0 ( System) has 73469 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 7294 elements [DEBUG ] Group 2 ( Protein-H) has 3716 elements [DEBUG ] Group 3 ( C-alpha) has 451 elements [DEBUG ] Group 4 ( Backbone) has 1353 elements [DEBUG ] Group 5 ( MainChain) has 1805 elements [DEBUG ] Group 6 ( MainChain+Cb) has 2220 elements [DEBUG ] Group 7 ( MainChain+H) has 2238 elements [DEBUG ] Group 8 ( SideChain) has 5056 elements [DEBUG ] Group 9 ( SideChain-H) has 1911 elements [DEBUG ] Group 10 ( Prot-Masses) has 7294 elements [DEBUG ] Group 11 ( non-Protein) has 66175 elements [DEBUG ] Group 12 ( Other) has 45 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 45 elements [DEBUG ] Group 14 ( K) has 55 elements [DEBUG ] Group 15 ( CL) has 45 elements [DEBUG ] Group 16 ( Water) has 66030 elements [DEBUG ] Group 17 ( SOL) has 66030 elements [DEBUG ] Group 18 ( non-Water) has 7439 elements [DEBUG ] Group 19 ( Ion) has 100 elements [DEBUG ] Group 20 ( CBI) has 45 elements [DEBUG ] Group 21 ( K) has 55 elements [DEBUG ] Group 22 ( CL) has 45 elements [DEBUG ] Group 23 ( Water_and_ions) has 66130 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 7339 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of K4R1CB.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: "Dreams seldom materialize on their own." (Dian Fossey) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 24: '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 1 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo 1 | /home/yxp212121/yxp/gmx2019/bin/gmx trjconv -f K4R1CB.xtc -s md.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2019.6 (-: [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 [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) 2001-2018, 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 2019.6 [DEBUG ] Executable: /home/yxp212121/yxp/gmx2019/bin/gmx [DEBUG ] Data prefix: /home/yxp212121/yxp/gmx2019 [DEBUG ] Working dir: /home/yxp212121/yxp/MMPBSA/Ks5A74R1jxmnCB-100ns-dt100ps-group0 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f K4R1CB.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 2019.6 (single precision) [DEBUG ] Reading file md.tpr, VERSION 2019.6 (single precision) [DEBUG ] Group 0 ( System) has 73469 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 7294 elements [DEBUG ] Group 2 ( Protein-H) has 3716 elements [DEBUG ] Group 3 ( C-alpha) has 451 elements [DEBUG ] Group 4 ( Backbone) has 1353 elements [DEBUG ] Group 5 ( MainChain) has 1805 elements [DEBUG ] Group 6 ( MainChain+Cb) has 2220 elements [DEBUG ] Group 7 ( MainChain+H) has 2238 elements [DEBUG ] Group 8 ( SideChain) has 5056 elements [DEBUG ] Group 9 ( SideChain-H) has 1911 elements [DEBUG ] Group 10 ( Prot-Masses) has 7294 elements [DEBUG ] Group 11 ( non-Protein) has 66175 elements [DEBUG ] Group 12 ( Other) has 45 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 45 elements [DEBUG ] Group 14 ( K) has 55 elements [DEBUG ] Group 15 ( CL) has 45 elements [DEBUG ] Group 16 ( Water) has 66030 elements [DEBUG ] Group 17 ( SOL) has 66030 elements [DEBUG ] Group 18 ( non-Water) has 7439 elements [DEBUG ] Group 19 ( Ion) has 100 elements [DEBUG ] Group 20 ( CBI) has 45 elements [DEBUG ] Group 21 ( K) has 55 elements [DEBUG ] Group 22 ( CL) has 45 elements [DEBUG ] Group 23 ( Water_and_ions) has 66130 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 7339 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of K4R1CB.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: "RTFM" (B. 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 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 13 in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo 13 | /home/yxp212121/yxp/gmx2019/bin/gmx trjconv -f K4R1CB.xtc -s md.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2019.6 (-: [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 [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) 2001-2018, 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 2019.6 [DEBUG ] Executable: /home/yxp212121/yxp/gmx2019/bin/gmx [DEBUG ] Data prefix: /home/yxp212121/yxp/gmx2019 [DEBUG ] Working dir: /home/yxp212121/yxp/MMPBSA/Ks5A74R1jxmnCB-100ns-dt100ps-group0 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f K4R1CB.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 2019.6 (single precision) [DEBUG ] Reading file md.tpr, VERSION 2019.6 (single precision) [DEBUG ] Group 0 ( System) has 73469 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 7294 elements [DEBUG ] Group 2 ( Protein-H) has 3716 elements [DEBUG ] Group 3 ( C-alpha) has 451 elements [DEBUG ] Group 4 ( Backbone) has 1353 elements [DEBUG ] Group 5 ( MainChain) has 1805 elements [DEBUG ] Group 6 ( MainChain+Cb) has 2220 elements [DEBUG ] Group 7 ( MainChain+H) has 2238 elements [DEBUG ] Group 8 ( SideChain) has 5056 elements [DEBUG ] Group 9 ( SideChain-H) has 1911 elements [DEBUG ] Group 10 ( Prot-Masses) has 7294 elements [DEBUG ] Group 11 ( non-Protein) has 66175 elements [DEBUG ] Group 12 ( Other) has 45 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 45 elements [DEBUG ] Group 14 ( K) has 55 elements [DEBUG ] Group 15 ( CL) has 45 elements [DEBUG ] Group 16 ( Water) has 66030 elements [DEBUG ] Group 17 ( SOL) has 66030 elements [DEBUG ] Group 18 ( non-Water) has 7439 elements [DEBUG ] Group 19 ( Ion) has 100 elements [DEBUG ] Group 20 ( CBI) has 45 elements [DEBUG ] Group 21 ( K) has 55 elements [DEBUG ] Group 22 ( CL) has 45 elements [DEBUG ] Group 23 ( Water_and_ions) has 66130 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 7339 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of K4R1CB.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: "Put Me Inside SSC, Let's Test Superstring Theory, Oh Yoi Yoi Accelerate the Protons" (Gogol Bordello) [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 Amber/OPLS force field topology format... [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Building Mutant Complex Topology... [INFO ] Mutating A/253 TRP by ALA [INFO ] Assigning PBRadii mbondi2 to Mutant Complex... [INFO ] Writing Mutant Complex AMBER topology... [INFO ] Detecting mutation in Receptor. Building Mutant Receptor topology... [INFO ] Assigning PBRadii mbondi2 to Mutant Receptor... [INFO ] Writing Mutant Receptor AMBER topology... [INFO ] Selecting residues by distance (6 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 38 residues: R:A:THR:13 R:A:SER:14 R:A:GLN:17 R:A:TRP:32 R:A:ARG:74 R:A:HIS:118 R:A:TRP:119 R:A:ASN:162 R:A:GLU:163 R:A:CYS:166 R:A:LEU:170 R:A:ILE:176 R:A:HIS:177 R:A:THR:220 R:A:CYS:221 R:A:GLY:222 R:A:TRP:253 R:A:ASN:300 R:A:ILE:301 R:A:TYR:302 R:A:ASN:303 R:A:MET:329 R:A:TRP:331 R:A:GLU:357 R:A:GLY:359 R:A:LEU:360 R:A:ALA:361 R:A:TRP:404 R:A:SER:405 R:A:ASN:409 R:A:PHE:410 R:A:GLU:411 R:A:TRP:412 R:A:ARG:413 R:A:GLU:414 R:A:LYS:418 R:A:PHE:420 L:B:CBI:453 [INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /home/yxp212121/yxp/gmx2019/bin/gmx trjconv -f K4R1CB.xtc -s md.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2019.6 (-: [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 [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) 2001-2018, 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 2019.6 [DEBUG ] Executable: /home/yxp212121/yxp/gmx2019/bin/gmx [DEBUG ] Data prefix: /home/yxp212121/yxp/gmx2019 [DEBUG ] Working dir: /home/yxp212121/yxp/MMPBSA/Ks5A74R1jxmnCB-100ns-dt100ps-group0 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f K4R1CB.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 2019.6 (single precision) [DEBUG ] Reading file md.tpr, VERSION 2019.6 (single precision) [DEBUG ] Group 0 ( System) has 73469 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 7294 elements [DEBUG ] Group 2 ( Protein-H) has 3716 elements [DEBUG ] Group 3 ( C-alpha) has 451 elements [DEBUG ] Group 4 ( Backbone) has 1353 elements [DEBUG ] Group 5 ( MainChain) has 1805 elements [DEBUG ] Group 6 ( MainChain+Cb) has 2220 elements [DEBUG ] Group 7 ( MainChain+H) has 2238 elements [DEBUG ] Group 8 ( SideChain) has 5056 elements [DEBUG ] Group 9 ( SideChain-H) has 1911 elements [DEBUG ] Group 10 ( Prot-Masses) has 7294 elements [DEBUG ] Group 11 ( non-Protein) has 66175 elements [DEBUG ] Group 12 ( Other) has 45 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 45 elements [DEBUG ] Group 14 ( K) has 55 elements [DEBUG ] Group 15 ( CL) has 45 elements [DEBUG ] Group 16 ( Water) has 66030 elements [DEBUG ] Group 17 ( SOL) has 66030 elements [DEBUG ] Group 18 ( non-Water) has 7439 elements [DEBUG ] Group 19 ( Ion) has 100 elements [DEBUG ] Group 20 ( CBI) has 45 elements [DEBUG ] Group 21 ( K) has 55 elements [DEBUG ] Group 22 ( CL) has 45 elements [DEBUG ] Group 23 ( Water_and_ions) has 66130 elements [DEBUG ] Group 24 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 7339 elements [DEBUG ] Select a group: Reading frame 0 time 0.000 [DEBUG ] Precision of K4R1CB.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "I always think there is something foreign about jolly phrases at breakfast." (Mr. Carson in Downtown Abbey) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 24: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] Building AMBER topologies from GROMACS files... Done. [INFO ] Loading and checking parameter files for compatibility... [INFO ] Preparing trajectories for simulation... [INFO ] Mutating trajectories... [INFO ] 1000 frames were processed by cpptraj for use in calculation. [INFO ] Running calculations on normal system... [INFO ] Beginning PB calculations with /home/yxp212121/yxp/amber20/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] calculating ligand contribution... [INFO ] Running calculations on mutant system... [INFO ] Beginning PB calculations with /home/yxp212121/yxp/amber20/bin/sander [INFO ] calculating complex contribution... [INFO ] calculating receptor contribution... [INFO ] no mutation found in ligand; using unmutated files [INFO ] Parsing results to output files...

Operating system

centos8 stream

gmx_MMPBSA Version

gmx_MMPBSA v1.5.6

Python version

python 3.9.7

Installation

AmberTools compilation + conda

Valdes-Tresanco-MS commented 2 years ago

I have not been able to reproduce the error. Can you send me a sample of your files (mmpbsa.in, md.tpr, index.ndx, 10 frames K4R1CB.xtc and topol.top + itps + charmm parm folder if it exists)

WXYWD commented 2 years ago

gmx_MMPBSA-files.zip These are my files and I hope this problem can be solved. Thank you!

Valdes-Tresanco-MS commented 2 years ago

For some reason, parmed does not process the topology. I suspect it is differences between the force fields folder, although I used several versions. Please send me the folder with the force field you used.

Valdes-Tresanco-MS commented 2 years ago

Closing due to inactivity. Reopen if necessary

Valdes-Tresanco-MS commented 2 years ago

Fixed via 8ca00d1