Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

[Bug-gmx_MMPBSA]: prmtop error #496

Open
overlord1647 opened this issue May 6, 2024 · 3 comments
Open

[Bug-gmx_MMPBSA]: prmtop error #496

overlord1647 opened this issue May 6, 2024 · 3 comments

Comments

@overlord1647
Copy link

Bug summary

i am running multi trajectory mmpbsa calculations using gmx_MMPBSA. i keep getting this error

Terminal output

$ gmx_MMPBSA -O -i mmpbsa.in -cs mmpbsa.tpr -ci index_c.ndx -cg 1 13 -ct mmpbsa.xtc -rs mt_p.tpr -ri index_p.ndx -rg 1 -rt prot.xtc  -ls mt_l.tpr  -li index_l.ndx -lg 2 -lt lig.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top  -rp topol_p.top -lp known_moldf_GMX_l.top
[INFO   ] Starting gmx_MMPBSA v1.6.3
[INFO   ] Command-line
  gmx_MMPBSA -O -i mmpbsa.in -cs mmpbsa.tpr -ci index_c.ndx -cg 1 13 -ct mmpbsa.xtc -rs mt_p.tpr -ri index_p.ndx -rg 1 -rt prot.xtc -ls mt_l.tpr -li index_l.ndx -lg 2 -lt lig.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top -rp topol_p.top -lp known_moldf_GMX_l.top

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO   ] Checking external programs...Done.

[INFO   ] Building AMBER topologies from GROMACS files...
[INFO   ] Get PDB files from GROMACS structures files...
[INFO   ] Making gmx_MMPBSA index for complex...
[INFO   ] Normal Complex: Saving group Protein_UNK (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[INFO   ] A receptor structure file was defined. Using MT approach...
[INFO   ] Making gmx_MMPBSA index for receptor...
[INFO   ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_REC_index.ndx file as _GMXMMPBSA_REC.pdb
[INFO   ] A ligand structure file was defined. Using MT approach...
[INFO   ] Making gmx_MMPBSA index for ligand...
[INFO   ] Normal Ligand: Saving group UNK (2) in _GMXMMPBSA_LIG_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 Amber/OPLS force field topology format...
[WARNING] 15 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO   ] Assigning PBRadii mbondi2 to Complex...
[INFO   ] Writing Normal Complex AMBER topology...
[INFO   ] A Receptor topology file was defined. Using MT approach...
[INFO   ] Building AMBER Receptor Topology from GROMACS Receptor Topology...
[INFO   ] Changing the Receptor residues name format from GROMACS to AMBER...
[WARNING] 6 invalid DIHEDRAL_PERIODICITY = 0 found in Receptor topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO   ] Assigning PBRadii mbondi2 to Receptor...
[INFO   ] Writing Normal Receptor AMBER topology...
[INFO   ] A Ligand Topology file was defined. Using MT approach...
[INFO   ] Building AMBER Ligand Topology from GROMACS Ligand Topology...
[INFO   ] Changing the Ligand residues name format from GROMACS to AMBER...
[WARNING] 9 invalid DIHEDRAL_PERIODICITY = 0 found in Ligand topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO   ] Assigning PBRadii mbondi2 to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Cleaning normal receptor trajectories...
[INFO   ] Cleaning normal ligand trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
  File "/home/rahool/anaconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/rahool/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/app.py", line 99, in gmxmmpbsa
    app.loadcheck_prmtops()
  File "/home/rahool/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/main.py", line 724, in loadcheck_prmtops
    self.normal_system.Map(INPUT['general']['receptor_mask'], INPUT['general']['ligand_mask'])
  File "/home/rahool/anaconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/parm_setup.py", line 174, in Map
    raise PrmtopError('Residue mismatch while mapping. ' +
PrmtopError: Residue mismatch while mapping. Incompatible topology files or bad mask definitions
Exiting. All files have been retained.

gmx_MMPBSA.log

[INFO ] Starting gmx_MMPBSA v1.6.3
[DEBUG ] WDIR : /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] AMBERHOME : /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] PYTHON EXE : /home/rahool/anaconda3/envs/gmxMMPBSA/bin/python
[DEBUG ] PYTHON VERSION: 3.9.19 | packaged by conda-forge | (main, Mar 20 2024, 12:50:21) [GCC 12.3.0]
[DEBUG ] MPI : /home/rahool/anaconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG ] ParmEd : 4.2.2
[DEBUG ] OS PLATFORM : Linux-3.10.0-1160.el7.x86_64-x86_64-with-glibc2.17
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #1 SMP Mon Oct 19 16:18:59 UTC 2020
[DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs mmpbsa.tpr -ci index_c.ndx -cg 1 13 -ct mmpbsa.xtc -rs mt_p.tpr -ri index_p.ndx -rg 1 -rt prot.xtc -ls mt_l.tpr -li index_l.ndx -lg 2 -lt lig.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv -cp topol.top -rp topol_p.top -lp known_moldf_GMX_l.top

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

[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[INFO ] Checking external programs...Done.

[INFO ] Building AMBER topologies from GROMACS files...
[INFO ] Get PDB files from GROMACS structures files...
[INFO ] Making gmx_MMPBSA index for complex...
[DEBUG ] Running command: echo -e "name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index_c.ndx -o _GMXMMPBSA_COM_index.ndx -f mmpbsa.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index_c.ndx -o _GMXMMPBSA_COM_index.ndx -f mmpbsa.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file mmpbsa.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mmpbsa.tpr, VERSION 5.1 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Theoretical chemistry has of course always been important and useful ... at least to theoretical chemists" (Sven Lidin)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 136433 atoms
[DEBUG ] 1 Protein : 3767 atoms
[DEBUG ] 2 Protein-H : 1887 atoms
[DEBUG ] 3 C-alpha : 234 atoms
[DEBUG ] 4 Backbone : 702 atoms
[DEBUG ] 5 MainChain : 937 atoms
[DEBUG ] 6 MainChain+Cb : 1160 atoms
[DEBUG ] 7 MainChain+H : 1167 atoms
[DEBUG ] 8 SideChain : 2600 atoms
[DEBUG ] 9 SideChain-H : 950 atoms
[DEBUG ] 10 Prot-Masses : 3767 atoms
[DEBUG ] 11 non-Protein : 132666 atoms
[DEBUG ] 12 Other : 36 atoms
[DEBUG ] 13 UNK : 36 atoms
[DEBUG ] 14 CL : 3 atoms
[DEBUG ] 15 Water : 132627 atoms
[DEBUG ] 16 SOL : 132627 atoms
[DEBUG ] 17 non-Water : 3806 atoms
[DEBUG ] 18 Ion : 3 atoms
[DEBUG ] 19 Water_and_ions : 132630 atoms
[DEBUG ] 20 Protein_UNK : 3803 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: 3767 36 -> 3803
[DEBUG ]
[DEBUG ] 21 GMXMMPBSA_REC_GMXMMPBSA_LIG: 3803 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_UNK (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f mmpbsa.xtc -s mmpbsa.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f mmpbsa.xtc -s mmpbsa.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file mmpbsa.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mmpbsa.tpr, VERSION 5.1 (single precision)
[DEBUG ] Group 0 ( System) has 136433 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3767 elements
[DEBUG ] Group 2 ( Protein-H) has 1887 elements
[DEBUG ] Group 3 ( C-alpha) has 234 elements
[DEBUG ] Group 4 ( Backbone) has 702 elements
[DEBUG ] Group 5 ( MainChain) has 937 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1160 elements
[DEBUG ] Group 7 ( MainChain+H) has 1167 elements
[DEBUG ] Group 8 ( SideChain) has 2600 elements
[DEBUG ] Group 9 ( SideChain-H) has 950 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3767 elements
[DEBUG ] Group 11 ( non-Protein) has 132666 elements
[DEBUG ] Group 12 ( Other) has 36 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 36 elements
[DEBUG ] Group 14 ( CL) has 3 elements
[DEBUG ] Group 15 ( Water) has 132627 elements
[DEBUG ] Group 16 ( SOL) has 132627 elements
[DEBUG ] Group 17 ( non-Water) has 3806 elements
[DEBUG ] Group 18 ( Ion) has 3 elements
[DEBUG ] Group 19 ( Water_and_ions) has 132630 elements
[DEBUG ] Group 20 ( Protein_UNK) has 3803 elements
[DEBUG ] Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 3803 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of mmpbsa.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Science Won't Change You" (The Talking Heads)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 21: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO ] A receptor structure file was defined. Using MT approach...
[INFO ] Making gmx_MMPBSA index for receptor...
[DEBUG ] Running command: echo -e "name 1 GMXMMPBSA_REC\n q\n" | /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index_p.ndx -o _GMXMMPBSA_REC_index.ndx -f mt_p.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index_p.ndx -o _GMXMMPBSA_REC_index.ndx -f mt_p.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file mt_p.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mt_p.tpr, VERSION 5.1 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Science Won't Change You" (The Talking Heads)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 86636 atoms
[DEBUG ] 1 Protein : 3767 atoms
[DEBUG ] 2 Protein-H : 1887 atoms
[DEBUG ] 3 C-alpha : 234 atoms
[DEBUG ] 4 Backbone : 702 atoms
[DEBUG ] 5 MainChain : 937 atoms
[DEBUG ] 6 MainChain+Cb : 1160 atoms
[DEBUG ] 7 MainChain+H : 1167 atoms
[DEBUG ] 8 SideChain : 2600 atoms
[DEBUG ] 9 SideChain-H : 950 atoms
[DEBUG ] 10 Prot-Masses : 3767 atoms
[DEBUG ] 11 non-Protein : 82869 atoms
[DEBUG ] 12 Water : 82866 atoms
[DEBUG ] 13 SOL : 82866 atoms
[DEBUG ] 14 non-Water : 3770 atoms
[DEBUG ] 15 Ion : 3 atoms
[DEBUG ] 16 Water_and_ions : 82869 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 ] >
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_REC_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo -e "1"| /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f prot.xtc -s mt_p.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_REC_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f prot.xtc -s mt_p.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_REC_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file mt_p.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mt_p.tpr, VERSION 5.1 (single precision)
[DEBUG ] Group 0 ( System) has 86636 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3767 elements
[DEBUG ] Group 2 ( Protein-H) has 1887 elements
[DEBUG ] Group 3 ( C-alpha) has 234 elements
[DEBUG ] Group 4 ( Backbone) has 702 elements
[DEBUG ] Group 5 ( MainChain) has 937 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1160 elements
[DEBUG ] Group 7 ( MainChain+H) has 1167 elements
[DEBUG ] Group 8 ( SideChain) has 2600 elements
[DEBUG ] Group 9 ( SideChain-H) has 950 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3767 elements
[DEBUG ] Group 11 ( non-Protein) has 82869 elements
[DEBUG ] Group 12 ( Water) has 82866 elements
[DEBUG ] Group 13 ( SOL) has 82866 elements
[DEBUG ] Group 14 ( non-Water) has 3770 elements
[DEBUG ] Group 15 ( Ion) has 3 elements
[DEBUG ] Group 16 ( Water_and_ions) has 82869 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of prot.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Science Won't Change You" (The Talking Heads)
[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 ] A ligand structure file was defined. Using MT approach...
[INFO ] Making gmx_MMPBSA index for ligand...
[DEBUG ] Running command: echo -e "name 2 GMXMMPBSA_LIG\n q\n" | /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index_l.ndx -o _GMXMMPBSA_LIG_index.ndx -f mt_l.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index_l.ndx -o _GMXMMPBSA_LIG_index.ndx -f mt_l.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file mt_l.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mt_l.tpr, VERSION 5.1 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Science Won't Change You" (The Talking Heads)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 3741 atoms
[DEBUG ] 1 Other : 36 atoms
[DEBUG ] 2 UNK : 36 atoms
[DEBUG ] 3 Water : 3705 atoms
[DEBUG ] 4 SOL : 3705 atoms
[DEBUG ] 5 non-Water : 36 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 ] >
[INFO ] Normal Ligand: Saving group UNK (2) in _GMXMMPBSA_LIG_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo -e "2"| /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f lig.xtc -s mt_l.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_LIG_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f lig.xtc -s mt_l.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_LIG_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file mt_l.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mt_l.tpr, VERSION 5.1 (single precision)
[DEBUG ] Group 0 ( System) has 3741 elements
[DEBUG ] Group 1 ( Other) has 36 elements
[DEBUG ] Group 2 ( GMXMMPBSA_LIG) has 36 elements
[DEBUG ] Group 3 ( Water) has 3705 elements
[DEBUG ] Group 4 ( SOL) has 3705 elements
[DEBUG ] Group 5 ( non-Water) has 36 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of lig.xtc is 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Science Won't Change You" (The Talking Heads)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 2: 'GMXMMPBSA_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...
[WARNING] 15 invalid DIHEDRAL_PERIODICITY = 0 found in Complex topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO ] Assigning PBRadii mbondi2 to Complex...
[INFO ] Writing Normal Complex AMBER topology...
[INFO ] A Receptor topology file was defined. Using MT approach...
[INFO ] Building AMBER Receptor Topology from GROMACS Receptor Topology...
[INFO ] Changing the Receptor residues name format from GROMACS to AMBER...
[WARNING] 6 invalid DIHEDRAL_PERIODICITY = 0 found in Receptor topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO ] Assigning PBRadii mbondi2 to Receptor...
[INFO ] Writing Normal Receptor AMBER topology...
[INFO ] A Ligand Topology file was defined. Using MT approach...
[INFO ] Building AMBER Ligand Topology from GROMACS Ligand Topology...
[INFO ] Changing the Ligand residues name format from GROMACS to AMBER...
[WARNING] 9 invalid DIHEDRAL_PERIODICITY = 0 found in Ligand topology... Setting DIHEDRAL_PERIODICITY = 1
[INFO ] Assigning PBRadii mbondi2 to Ligand...
[INFO ] Writing Normal Ligand AMBER topology...
[INFO ] Cleaning normal complex trajectories...
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f mmpbsa.xtc -s mmpbsa.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f mmpbsa.xtc -s mmpbsa.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 mmpbsa.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mmpbsa.tpr, VERSION 5.1 (single precision)
[DEBUG ] Group 0 ( System) has 136433 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3767 elements
[DEBUG ] Group 2 ( Protein-H) has 1887 elements
[DEBUG ] Group 3 ( C-alpha) has 234 elements
[DEBUG ] Group 4 ( Backbone) has 702 elements
[DEBUG ] Group 5 ( MainChain) has 937 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1160 elements
[DEBUG ] Group 7 ( MainChain+H) has 1167 elements
[DEBUG ] Group 8 ( SideChain) has 2600 elements
[DEBUG ] Group 9 ( SideChain-H) has 950 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3767 elements
[DEBUG ] Group 11 ( non-Protein) has 132666 elements
[DEBUG ] Group 12 ( Other) has 36 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 36 elements
[DEBUG ] Group 14 ( CL) has 3 elements
[DEBUG ] Group 15 ( Water) has 132627 elements
[DEBUG ] Group 16 ( SOL) has 132627 elements
[DEBUG ] Group 17 ( non-Water) has 3806 elements
[DEBUG ] Group 18 ( Ion) has 3 elements
[DEBUG ] Group 19 ( Water_and_ions) has 132630 elements
[DEBUG ] Group 20 ( Protein_UNK) has 3803 elements
[DEBUG ] Group 21 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 3803 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of mmpbsa.xtc is 0.001 (nm)
[DEBUG ] Using output precision of 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000 -> frame 0 time 0.000

Reading frame 2 time 200.000 -> frame 1 time 100.000

Reading frame 3 time 300.000 -> frame 2 time 200.000

Reading frame 4 time 400.000 -> frame 3 time 300.000

Reading frame 5 time 500.000 -> frame 4 time 400.000

Reading frame 6 time 600.000 -> frame 5 time 500.000

Reading frame 7 time 700.000 -> frame 6 time 600.000

Reading frame 8 time 800.000 -> frame 7 time 700.000

Reading frame 9 time 900.000 -> frame 8 time 800.000

Reading frame 10 time 1000.000 -> frame 9 time 900.000

Reading frame 11 time 1100.000 -> frame 10 time 1000.000

Reading frame 12 time 1200.000 -> frame 11 time 1100.000

Reading frame 13 time 1300.000 -> frame 12 time 1200.000

Reading frame 14 time 1400.000 -> frame 13 time 1300.000

Reading frame 15 time 1500.000 -> frame 14 time 1400.000

Reading frame 16 time 1600.000 -> frame 15 time 1500.000

Reading frame 17 time 1700.000 -> frame 16 time 1600.000

Reading frame 18 time 1800.000 -> frame 17 time 1700.000

Reading frame 19 time 1900.000 -> frame 18 time 1800.000

Reading frame 20 time 2000.000 -> frame 19 time 1900.000

Reading frame 30 time 3000.000 -> frame 29 time 2900.000

Reading frame 40 time 4000.000 -> frame 39 time 3900.000

Reading frame 50 time 5000.000 -> frame 49 time 4900.000

Reading frame 60 time 6000.000 -> frame 59 time 5900.000

Reading frame 70 time 7000.000 -> frame 69 time 6900.000

Reading frame 80 time 8000.000 -> frame 79 time 7900.000

Reading frame 90 time 9000.000 -> frame 89 time 8900.000

Reading frame 100 time 10000.000 -> frame 99 time 9900.000

Reading frame 110 time 11000.000 -> frame 109 time 10900.000

Reading frame 120 time 12000.000 -> frame 119 time 11900.000

Reading frame 130 time 13000.000 -> frame 129 time 12900.000

Reading frame 140 time 14000.000 -> frame 139 time 13900.000

Reading frame 150 time 15000.000 -> frame 149 time 14900.000

Reading frame 160 time 16000.000 -> frame 159 time 15900.000

Reading frame 170 time 17000.000 -> frame 169 time 16900.000

Reading frame 180 time 18000.000 -> frame 179 time 17900.000

Reading frame 190 time 19000.000 -> frame 189 time 18900.000

Reading frame 200 time 20000.000 -> frame 199 time 19900.000

Reading frame 300 time 30000.000 -> frame 299 time 29900.000

Reading frame 400 time 40000.000 -> frame 399 time 39900.000

Reading frame 500 time 50000.000 -> frame 499 time 49900.000

Last frame 500 time 50000.000
[DEBUG ] Last written: frame 500 time 50000.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Problems worthy of attack prove their worth by hitting back." (Piet Hein)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 21: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO ] Cleaning normal receptor trajectories...
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC"| /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f prot.xtc -s mt_p.tpr -o REC_traj_0.xtc -n _GMXMMPBSA_REC_index.ndx
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f prot.xtc -s mt_p.tpr -o REC_traj_0.xtc -n _GMXMMPBSA_REC_index.ndx
[DEBUG ]
[DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG ] Reading file mt_p.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mt_p.tpr, VERSION 5.1 (single precision)
[DEBUG ] Group 0 ( System) has 86636 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 3767 elements
[DEBUG ] Group 2 ( Protein-H) has 1887 elements
[DEBUG ] Group 3 ( C-alpha) has 234 elements
[DEBUG ] Group 4 ( Backbone) has 702 elements
[DEBUG ] Group 5 ( MainChain) has 937 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 1160 elements
[DEBUG ] Group 7 ( MainChain+H) has 1167 elements
[DEBUG ] Group 8 ( SideChain) has 2600 elements
[DEBUG ] Group 9 ( SideChain-H) has 950 elements
[DEBUG ] Group 10 ( Prot-Masses) has 3767 elements
[DEBUG ] Group 11 ( non-Protein) has 82869 elements
[DEBUG ] Group 12 ( Water) has 82866 elements
[DEBUG ] Group 13 ( SOL) has 82866 elements
[DEBUG ] Group 14 ( non-Water) has 3770 elements
[DEBUG ] Group 15 ( Ion) has 3 elements
[DEBUG ] Group 16 ( Water_and_ions) has 82869 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of prot.xtc is 0.001 (nm)
[DEBUG ] Using output precision of 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000 -> frame 0 time 0.000

Reading frame 2 time 200.000 -> frame 1 time 100.000

Reading frame 3 time 300.000 -> frame 2 time 200.000

Reading frame 4 time 400.000 -> frame 3 time 300.000

Reading frame 5 time 500.000 -> frame 4 time 400.000

Reading frame 6 time 600.000 -> frame 5 time 500.000

Reading frame 7 time 700.000 -> frame 6 time 600.000

Reading frame 8 time 800.000 -> frame 7 time 700.000

Reading frame 9 time 900.000 -> frame 8 time 800.000

Reading frame 10 time 1000.000 -> frame 9 time 900.000

Reading frame 11 time 1100.000 -> frame 10 time 1000.000

Reading frame 12 time 1200.000 -> frame 11 time 1100.000

Reading frame 13 time 1300.000 -> frame 12 time 1200.000

Reading frame 14 time 1400.000 -> frame 13 time 1300.000

Reading frame 15 time 1500.000 -> frame 14 time 1400.000

Reading frame 16 time 1600.000 -> frame 15 time 1500.000

Reading frame 17 time 1700.000 -> frame 16 time 1600.000

Reading frame 18 time 1800.000 -> frame 17 time 1700.000

Reading frame 19 time 1900.000 -> frame 18 time 1800.000

Reading frame 20 time 2000.000 -> frame 19 time 1900.000

Reading frame 30 time 3000.000 -> frame 29 time 2900.000

Reading frame 40 time 4000.000 -> frame 39 time 3900.000

Reading frame 50 time 5000.000 -> frame 49 time 4900.000

Reading frame 60 time 6000.000 -> frame 59 time 5900.000

Reading frame 70 time 7000.000 -> frame 69 time 6900.000

Reading frame 80 time 8000.000 -> frame 79 time 7900.000

Reading frame 90 time 9000.000 -> frame 89 time 8900.000

Reading frame 100 time 10000.000 -> frame 99 time 9900.000

Reading frame 110 time 11000.000 -> frame 109 time 10900.000

Reading frame 120 time 12000.000 -> frame 119 time 11900.000

Reading frame 130 time 13000.000 -> frame 129 time 12900.000

Reading frame 140 time 14000.000 -> frame 139 time 13900.000

Reading frame 150 time 15000.000 -> frame 149 time 14900.000

Reading frame 160 time 16000.000 -> frame 159 time 15900.000

Reading frame 170 time 17000.000 -> frame 169 time 16900.000

Reading frame 180 time 18000.000 -> frame 179 time 17900.000

Reading frame 190 time 19000.000 -> frame 189 time 18900.000

Reading frame 200 time 20000.000 -> frame 199 time 19900.000

Reading frame 300 time 30000.000 -> frame 299 time 29900.000

Reading frame 400 time 40000.000 -> frame 399 time 39900.000

Reading frame 500 time 50000.000 -> frame 499 time 49900.000

Last frame 500 time 50000.000
[DEBUG ] Last written: frame 500 time 50000.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Humbug! Most things free-born will submit to anything for a salary" (Mr. Rochester in Jane Eyre by Charlotte Bronte)
[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 ] Cleaning normal ligand trajectories...
[DEBUG ] Running command: echo -e "GMXMMPBSA_LIG"| /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f lig.xtc -s mt_l.tpr -o LIG_traj_0.xtc -n _GMXMMPBSA_LIG_index.ndx
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.1-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/rahool/anaconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/rahool/anaconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/rahool/trar/mmpbsa_mt/known_mt
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f lig.xtc -s mt_l.tpr -o LIG_traj_0.xtc -n _GMXMMPBSA_LIG_index.ndx
[DEBUG ]
[DEBUG ] Will write xtc: Compressed trajectory (portable xdr format): xtc
[DEBUG ] Reading file mt_l.tpr, VERSION 5.1 (single precision)
[DEBUG ] Reading file mt_l.tpr, VERSION 5.1 (single precision)
[DEBUG ] Group 0 ( System) has 3741 elements
[DEBUG ] Group 1 ( Other) has 36 elements
[DEBUG ] Group 2 ( GMXMMPBSA_LIG) has 36 elements
[DEBUG ] Group 3 ( Water) has 3705 elements
[DEBUG ] Group 4 ( SOL) has 3705 elements
[DEBUG ] Group 5 ( non-Water) has 36 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of lig.xtc is 0.001 (nm)
[DEBUG ] Using output precision of 0.001 (nm)
[DEBUG ]
Reading frame 1 time 100.000 -> frame 0 time 0.000

Reading frame 2 time 200.000 -> frame 1 time 100.000

Reading frame 3 time 300.000 -> frame 2 time 200.000

Reading frame 4 time 400.000 -> frame 3 time 300.000

Reading frame 5 time 500.000 -> frame 4 time 400.000

Reading frame 6 time 600.000 -> frame 5 time 500.000

Reading frame 7 time 700.000 -> frame 6 time 600.000

Reading frame 8 time 800.000 -> frame 7 time 700.000

Reading frame 9 time 900.000 -> frame 8 time 800.000

Reading frame 10 time 1000.000 -> frame 9 time 900.000

Reading frame 11 time 1100.000 -> frame 10 time 1000.000

Reading frame 12 time 1200.000 -> frame 11 time 1100.000

Reading frame 13 time 1300.000 -> frame 12 time 1200.000

Reading frame 14 time 1400.000 -> frame 13 time 1300.000

Reading frame 15 time 1500.000 -> frame 14 time 1400.000

Reading frame 16 time 1600.000 -> frame 15 time 1500.000

Reading frame 17 time 1700.000 -> frame 16 time 1600.000

Reading frame 18 time 1800.000 -> frame 17 time 1700.000

Reading frame 19 time 1900.000 -> frame 18 time 1800.000

Reading frame 20 time 2000.000 -> frame 19 time 1900.000

Reading frame 30 time 3000.000 -> frame 29 time 2900.000

Reading frame 40 time 4000.000 -> frame 39 time 3900.000

Reading frame 50 time 5000.000 -> frame 49 time 4900.000

Reading frame 60 time 6000.000 -> frame 59 time 5900.000

Reading frame 70 time 7000.000 -> frame 69 time 6900.000

Reading frame 80 time 8000.000 -> frame 79 time 7900.000

Reading frame 90 time 9000.000 -> frame 89 time 8900.000

Reading frame 100 time 10000.000 -> frame 99 time 9900.000

Reading frame 110 time 11000.000 -> frame 109 time 10900.000

Reading frame 120 time 12000.000 -> frame 119 time 11900.000

Reading frame 130 time 13000.000 -> frame 129 time 12900.000

Reading frame 140 time 14000.000 -> frame 139 time 13900.000

Reading frame 150 time 15000.000 -> frame 149 time 14900.000

Reading frame 160 time 16000.000 -> frame 159 time 15900.000

Reading frame 170 time 17000.000 -> frame 169 time 16900.000

Reading frame 180 time 18000.000 -> frame 179 time 17900.000

Reading frame 190 time 19000.000 -> frame 189 time 18900.000

Reading frame 200 time 20000.000 -> frame 199 time 19900.000

Reading frame 300 time 30000.000 -> frame 299 time 29900.000

Reading frame 400 time 40000.000 -> frame 399 time 39900.000

Reading frame 500 time 50000.000 -> frame 499 time 49900.000

Last frame 500 time 50000.000
[DEBUG ] Last written: frame 500 time 50000.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "Humbug! Most things free-born will submit to anything for a salary" (Mr. Rochester in Jane Eyre by Charlotte Bronte)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 2: 'GMXMMPBSA_LIG'
[INFO ] Building AMBER topologies from GROMACS files... Done.

[INFO ] Loading and checking parameter files for compatibility...

Operating system

CentOS Linux 7

gmx_MMPBSA Version

1.6.3

Python version

Python 3.9.19

Installation

pip
@Valdes-Tresanco-MS
Copy link
Owner

Do you get this error only for your system or does it happen as well with the MTP example

@overlord1647
Copy link
Author

error happens only for my system

@marioernestovaldes
Copy link
Collaborator

could you please the files you are using?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

No branches or pull requests
3 participants
@Valdes-Tresanco-MS @marioernestovaldes @overlord1647