Mario Sergio Valdes
Hi AMBER users,
I have a problem with running tleap im gmxMMPBSA calculation.
In this, it is adding two extra atoms that missing heavy atoms but in my created system having gromos54a7 forcefield, there is no missing atoms.
I would greatly appreciate if you could give a solution for this problem.
Thanks in advance.
[INFO ] Starting gmx_MMPBSA v1.6.1+16.gc99f0b4
[DEBUG ] WDIR : /home/ad2/Desktop/Luteolin/MD/complex/npt_withoutposre/npt_10ns_310K/extend-100ns/extend-140/extend-150/extend-3000ns/mmpbsa
[DEBUG ] AMBERHOME : /home/ad2/miniconda3/envs/gmxMMPBSA
[DEBUG ] PYTHON EXE : /home/ad2/miniconda3/envs/gmxMMPBSA/bin/python
[DEBUG ] PYTHON VERSION: 3.9.12 | packaged by conda-forge | (main, Mar 24 2022, 23:25:59) [GCC 10.3.0]
[DEBUG ] MPI : /home/ad2/miniconda3/envs/gmxMMPBSA/bin/mpirun
[DEBUG ] ParmEd : 3.4.3+11.g41cc9ab
[DEBUG ] OS PLATFORM : Linux-5.4.0-148-generic-x86_64-with-glibc2.27
[DEBUG ] OS SYSTEM : Linux
[DEBUG ] OS VERSION : #165~18.04.1-Ubuntu SMP Thu Apr 20 01:14:06 UTC 2023
[DEBUG ] OS PROCESSOR : x86_64
[INFO ] Command-line
gmx_MMPBSA -nogui -O -i mmpbsa.in -cs npt.tpr -ci index.ndx -eo Interaction_energy.csv -cg 4 19 -lm molecule.mol2 -ct new.trr
[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 = "System" # 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 = "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 = 310 # 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 = "/home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256" # 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 ] |
[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 = 4.0 # 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 = 0 # 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 ]
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /home/ad2/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO ] tleap found! Using /home/ad2/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO ] parmchk2 found! Using /home/ad2/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO ] sander found! Using /home/ad2/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /home/ad2/miniconda3/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 4 GMXMMPBSA_REC\n name 19 GMXMMPBSA_LIG\n 4 | 19\n q\n" | /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f npt.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2022.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/ad2/miniconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/ad2/Desktop/Luteolin/MD/complex/npt_withoutposre/npt_10ns_310K/extend-100ns/extend-140/extend-150/extend-3000ns/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f npt.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "I identified myself very early on as a scientist rather than a student - as someone creating knowledge rather than simply absorbing it." (Emmanuelle Charpentier)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 8609 atoms
[DEBUG ] 1 Other : 31 atoms
[DEBUG ] 2 BTVL : 31 atoms
[DEBUG ] 3 NA : 2 atoms
[DEBUG ] 4 Protein : 890 atoms
[DEBUG ] 5 Protein-H : 706 atoms
[DEBUG ] 6 C-alpha : 91 atoms
[DEBUG ] 7 Backbone : 273 atoms
[DEBUG ] 8 MainChain : 365 atoms
[DEBUG ] 9 MainChain+Cb : 449 atoms
[DEBUG ] 10 MainChain+H : 456 atoms
[DEBUG ] 11 SideChain : 434 atoms
[DEBUG ] 12 SideChain-H : 341 atoms
[DEBUG ] 13 Prot-Masses : 890 atoms
[DEBUG ] 14 non-Protein : 7719 atoms
[DEBUG ] 15 Water : 7686 atoms
[DEBUG ] 16 SOL : 7686 atoms
[DEBUG ] 17 non-Water : 923 atoms
[DEBUG ] 18 Ion : 2 atoms
[DEBUG ] 19 BTVL : 31 atoms
[DEBUG ] 20 NA : 2 atoms
[DEBUG ] 21 Water_and_ions : 7688 atoms
[DEBUG ] 22 System : 8609 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 4 'GMXMMPBSA_REC'
[DEBUG ] Copied index group 19 'GMXMMPBSA_LIG'
[DEBUG ] Merged two groups with OR: 890 31 -> 921
[DEBUG ]
[DEBUG ] 23 GMXMMPBSA_REC_GMXMMPBSA_LIG: 921 atoms
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_BTVL (4_19) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f new.trr -s npt.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/ad2/miniconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/ad2/Desktop/Luteolin/MD/complex/npt_withoutposre/npt_10ns_310K/extend-100ns/extend-140/extend-150/extend-3000ns/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f new.trr -s npt.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Group 0 ( System) has 8609 elements
[DEBUG ] Group 1 ( Other) has 31 elements
[DEBUG ] Group 2 ( BTVL) has 31 elements
[DEBUG ] Group 3 ( NA) has 2 elements
[DEBUG ] Group 4 ( GMXMMPBSA_REC) has 890 elements
[DEBUG ] Group 5 ( Protein-H) has 706 elements
[DEBUG ] Group 6 ( C-alpha) has 91 elements
[DEBUG ] Group 7 ( Backbone) has 273 elements
[DEBUG ] Group 8 ( MainChain) has 365 elements
[DEBUG ] Group 9 ( MainChain+Cb) has 449 elements
[DEBUG ] Group 10 ( MainChain+H) has 456 elements
[DEBUG ] Group 11 ( SideChain) has 434 elements
[DEBUG ] Group 12 ( SideChain-H) has 341 elements
[DEBUG ] Group 13 ( Prot-Masses) has 890 elements
[DEBUG ] Group 14 ( non-Protein) has 7719 elements
[DEBUG ] Group 15 ( Water) has 7686 elements
[DEBUG ] Group 16 ( SOL) has 7686 elements
[DEBUG ] Group 17 ( non-Water) has 923 elements
[DEBUG ] Group 18 ( Ion) has 2 elements
[DEBUG ] Group 19 ( GMXMMPBSA_LIG) has 31 elements
[DEBUG ] Group 20 ( NA) has 2 elements
[DEBUG ] Group 21 ( Water_and_ions) has 7688 elements
[DEBUG ] Group 22 ( System) has 8609 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 921 elements
[DEBUG ] Select a group: trr version: GMX_trn_file (single precision)
[DEBUG ]
Reading frame 0 time 0.000
Reading frame 1 time 500.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "I identified myself very early on as a scientist rather than a student - as someone creating knowledge rather than simply absorbing it." (Emmanuelle Charpentier)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 23: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO ] Generating ligand parameters from molecule.mol2 file...
[DEBUG ] Running command: /home/ad2/miniconda3/envs/gmxMMPBSA/bin/parmchk2 -i molecule.mol2 -f mol2 -o _GMXMMPBSA_molecule.frcmod -s 1
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (4) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo -e "4"| /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f new.trr -s npt.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/ad2/miniconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/ad2/Desktop/Luteolin/MD/complex/npt_withoutposre/npt_10ns_310K/extend-100ns/extend-140/extend-150/extend-3000ns/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f new.trr -s npt.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Group 0 ( System) has 8609 elements
[DEBUG ] Group 1 ( Other) has 31 elements
[DEBUG ] Group 2 ( BTVL) has 31 elements
[DEBUG ] Group 3 ( NA) has 2 elements
[DEBUG ] Group 4 ( GMXMMPBSA_REC) has 890 elements
[DEBUG ] Group 5 ( Protein-H) has 706 elements
[DEBUG ] Group 6 ( C-alpha) has 91 elements
[DEBUG ] Group 7 ( Backbone) has 273 elements
[DEBUG ] Group 8 ( MainChain) has 365 elements
[DEBUG ] Group 9 ( MainChain+Cb) has 449 elements
[DEBUG ] Group 10 ( MainChain+H) has 456 elements
[DEBUG ] Group 11 ( SideChain) has 434 elements
[DEBUG ] Group 12 ( SideChain-H) has 341 elements
[DEBUG ] Group 13 ( Prot-Masses) has 890 elements
[DEBUG ] Group 14 ( non-Protein) has 7719 elements
[DEBUG ] Group 15 ( Water) has 7686 elements
[DEBUG ] Group 16 ( SOL) has 7686 elements
[DEBUG ] Group 17 ( non-Water) has 923 elements
[DEBUG ] Group 18 ( Ion) has 2 elements
[DEBUG ] Group 19 ( GMXMMPBSA_LIG) has 31 elements
[DEBUG ] Group 20 ( NA) has 2 elements
[DEBUG ] Group 21 ( Water_and_ions) has 7688 elements
[DEBUG ] Group 22 ( System) has 8609 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 921 elements
[DEBUG ] Select a group: trr version: GMX_trn_file (single precision)
[DEBUG ]
Reading frame 0 time 0.000
Reading frame 1 time 500.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "I identified myself very early on as a scientist rather than a student - as someone creating knowledge rather than simply absorbing it." (Emmanuelle Charpentier)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 4: '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 BTVL (19) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo -e "19"| /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f new.trr -s npt.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2022.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /home/ad2/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /home/ad2/miniconda3/envs/gmxMMPBSA
[DEBUG ] Working dir: /home/ad2/Desktop/Luteolin/MD/complex/npt_withoutposre/npt_10ns_310K/extend-100ns/extend-140/extend-150/extend-3000ns/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f new.trr -s npt.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ]
[DEBUG ] Will write pdb: Protein data bank file
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Reading file npt.tpr, VERSION 2018.1 (single precision)
[DEBUG ] Group 0 ( System) has 8609 elements
[DEBUG ] Group 1 ( Other) has 31 elements
[DEBUG ] Group 2 ( BTVL) has 31 elements
[DEBUG ] Group 3 ( NA) has 2 elements
[DEBUG ] Group 4 ( GMXMMPBSA_REC) has 890 elements
[DEBUG ] Group 5 ( Protein-H) has 706 elements
[DEBUG ] Group 6 ( C-alpha) has 91 elements
[DEBUG ] Group 7 ( Backbone) has 273 elements
[DEBUG ] Group 8 ( MainChain) has 365 elements
[DEBUG ] Group 9 ( MainChain+Cb) has 449 elements
[DEBUG ] Group 10 ( MainChain+H) has 456 elements
[DEBUG ] Group 11 ( SideChain) has 434 elements
[DEBUG ] Group 12 ( SideChain-H) has 341 elements
[DEBUG ] Group 13 ( Prot-Masses) has 890 elements
[DEBUG ] Group 14 ( non-Protein) has 7719 elements
[DEBUG ] Group 15 ( Water) has 7686 elements
[DEBUG ] Group 16 ( SOL) has 7686 elements
[DEBUG ] Group 17 ( non-Water) has 923 elements
[DEBUG ] Group 18 ( Ion) has 2 elements
[DEBUG ] Group 19 ( GMXMMPBSA_LIG) has 31 elements
[DEBUG ] Group 20 ( NA) has 2 elements
[DEBUG ] Group 21 ( Water_and_ions) has 7688 elements
[DEBUG ] Group 22 ( System) has 8609 elements
[DEBUG ] Group 23 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 921 elements
[DEBUG ] Select a group: trr version: GMX_trn_file (single precision)
[DEBUG ]
Reading frame 0 time 0.000
Reading frame 1 time 500.000
[DEBUG ] Dumping frame at t= 0 ps
[DEBUG ] Last written: frame 0 time 0.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "I identified myself very early on as a scientist rather than a student - as someone creating knowledge rather than simply absorbing it." (Emmanuelle Charpentier)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 19: 'GMXMMPBSA_LIG'
[INFO ] Checking the structures consistency...
[INFO ]
[INFO ] Generating AMBER Compatible PDB Files...
[INFO ] Changing the Complex residues name format from GROMACS to AMBER...
[INFO ] Changing the Receptor residues name format from GROMACS to AMBER...
[INFO ] Changing the Ligand residues name format from GROMACS to AMBER...
[INFO ] Splitting receptor and ligand in PDB files..
[INFO ] Building tleap input files...
[DEBUG ] -I: Adding /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/prep to search path.
[DEBUG ] -I: Adding /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib to search path.
[DEBUG ] -I: Adding /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/parm to search path.
[DEBUG ] -I: Adding /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/cmd to search path.
[DEBUG ] -f: Source _GMXMMPBSA_leap.in.
[DEBUG ] -I: Adding /home/ad2/miniconda3/envs/gmxMMPBSA/lib/python3.9/site-packages/GMXMMPBSA/data to search path.
[DEBUG ]
[DEBUG ] Welcome to LEaP!
[DEBUG ] (no leaprc in search path)
[DEBUG ] Sourcing: ./_GMXMMPBSA_leap.in
[DEBUG ] ----- Source: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/oldff/leaprc.ff99SB
[DEBUG ] ----- Source of /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/oldff/leaprc.ff99SB done
[DEBUG ] Log file: ./leap.log
[DEBUG ] Loading parameters: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/parm/parm99.dat
[DEBUG ] Reading title:
[DEBUG ] PARM99 for DNA,RNA,AA, organic molecules, Polariz.& LP incl.02/04/99
[DEBUG ] Loading parameters: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/parm/frcmod.ff99SB
[DEBUG ] Reading force field modification type file (frcmod)
[DEBUG ] Reading title:
[DEBUG ] Modification/update of parm99.dat (Hornak & Simmerling)
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_nucleic94.lib
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_amino94.lib
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_aminoct94.lib
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/all_aminont94.lib
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/ions94.lib
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/solvents.lib
[DEBUG ] ----- Source: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/leaprc.gaff
[DEBUG ] ----- Source of /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/cmd/leaprc.gaff done
[DEBUG ] Log file: ./leap.log
[DEBUG ] Loading parameters: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/parm/gaff.dat
[DEBUG ] Reading title:
[DEBUG ] AMBER General Force Field for organic molecules (Version 1.81, May 2017)
[DEBUG ] Loading library: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/lib/atomic_ions.lib
[DEBUG ] Loading parameters: /home/ad2/miniconda3/envs/gmxMMPBSA/dat/leap/parm/frcmod.ions234lm_126_tip3p
[DEBUG ] Reading force field modification type file (frcmod)
[DEBUG ] Reading title:
[DEBUG ] Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
[DEBUG ] Using H(N)-modified Bondi radii
[DEBUG ] Loading PDB file: ./_GMXMMPBSA_REC_F1.pdb
[DEBUG ] Created a new atom named: O1 within residue: .R<CGLN 91>
[DEBUG ] Created a new atom named: O2 within residue: .R<CGLN 91>
[DEBUG ] Added missing heavy atom: .R<CGLN 91>.A<O 17>
[DEBUG ] Added missing heavy atom: .R<CGLN 91>.A<OXT 18>
[DEBUG ] total atoms in file: 706
[DEBUG ] Leap added 732 missing atoms according to residue templates:
[DEBUG ] 2 Heavy
[DEBUG ] 730 H / lone pairs
[DEBUG ] The file contained 2 atoms not in residue templates
[DEBUG ] Loading Mol2 file: ./molecule.mol2
[DEBUG ] Reading MOLECULE named BTV
[DEBUG ] Loading parameters: ./_GMXMMPBSA_molecule.frcmod
[DEBUG ] Reading force field modification type file (frcmod)
[DEBUG ] Reading title:
[DEBUG ] Remark line goes here
[DEBUG ] Checking 'LIG1'....
[DEBUG ] Checking parameters for unit 'LIG1'.
[DEBUG ] Checking for bond parameters.
[DEBUG ] Checking for angle parameters.
[DEBUG ] Unit is OK.
[DEBUG ] Checking Unit.
[DEBUG ] Building topology.
[DEBUG ] Building atom parameters.
[DEBUG ] Building bond parameters.
[DEBUG ] Building angle parameters.
[DEBUG ] Building proper torsion parameters.
[DEBUG ] Building improper torsion parameters.
[DEBUG ] total 15 improper torsions applied
[DEBUG ] Building H-Bond parameters.
[DEBUG ] Incorporating Non-Bonded adjustments.
[DEBUG ] Not Marking per-residue atom chain types.
[DEBUG ] Marking per-residue atom chain types.
[DEBUG ] (Residues lacking connect0/connect1 -
[DEBUG ] these don't have chain types marked:
[DEBUG ]
[DEBUG ] res total affected
[DEBUG ]
[DEBUG ] BTV 1
[DEBUG ] )
[DEBUG ] (no restraints)
[DEBUG ] Checking Unit.
[DEBUG ]
[DEBUG ] /home/ad2/miniconda3/envs/gmxMMPBSA/bin/teLeap: Warning!
[DEBUG ] The unperturbed charge of the unit (-2.000000) is not zero.
[DEBUG ] FATAL: Atom .R<CGLN 91>.A<O2 20> does not have a type.
[DEBUG ] FATAL: Atom .R<CGLN 91>.A<O1 19> does not have a type.
[DEBUG ]
[DEBUG ] /home/ad2/miniconda3/envs/gmxMMPBSA/bin/teLeap: Fatal Error!
[DEBUG ] Failed to generate parameters
[DEBUG ]
[DEBUG ] Exiting LEaP: Errors = 1; Warnings = 1; Notes = 0.
[ERROR ] MMPBSA_Error
/home/ad2/miniconda3/envs/gmxMMPBSA/bin/tleap failed when querying _GMXMMPBSA_leap.in
Check the gmx_MMPBSA.log file to report the problem.--
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