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gmx_MMPBSA.log
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gmx_MMPBSA.log
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[INFO ] Starting gmx_MMPBSA v1.6.3
[DEBUG ] WDIR : /Users/imac/Desktop/Simulation/protein-ligand/mmpbsa
[DEBUG ] AMBERHOME : /Users/imac/anaconda3/envs/mm
[DEBUG ] PYTHON EXE : /Users/imac/anaconda3/envs/mm/bin/python
[DEBUG ] PYTHON VERSION: 3.9.19 | packaged by conda-forge | (main, Mar 20 2024, 12:53:33) [Clang 16.0.6 ]
[DEBUG ] MPI : /Users/imac/anaconda3/envs/mm/bin/mpirun
[DEBUG ] ParmEd : 4.2.2
[DEBUG ] OS PLATFORM : macOS-13.6.9-x86_64-i386-64bit
[DEBUG ] OS SYSTEM : Darwin
[DEBUG ] OS VERSION : Darwin Kernel Version 22.6.0: Mon Jun 24 01:25:37 PDT 2024; root:xnu-8796.141.3.706.2~1/RELEASE_X86_64
[DEBUG ] OS PROCESSOR : i386
[INFO ] Command-line
gmx_MMPBSA -O -i mmpbsa.in -cs md_0_100.tpr -ct md_0_100_fit.xtc -ci index.ndx -cg 1 13 -cp topol.top -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv
[DEBUG ] |Input file:
[DEBUG ] |--------------------------------------------------------------
[DEBUG ] |GB calculation
[DEBUG ] |
[DEBUG ] |&general
[DEBUG ] |sys_name="Prot-Lig",
[DEBUG ] |startframe=1,
[DEBUG ] |endframe=100,
[DEBUG ] |/
[DEBUG ] |&gb
[DEBUG ] |igb=5, saltcon=0.150,
[DEBUG ] |/--------------------------------------------------------------
[DEBUG ]
[INFO ] Checking mmpbsa.in input file...
[INFO ] Checking mmpbsa.in input file...Done.
[INFO ] Checking external programs...
[INFO ] cpptraj found! Using /Users/imac/anaconda3/envs/mm/bin/cpptraj
[INFO ] tleap found! Using /Users/imac/anaconda3/envs/mm/bin/tleap
[INFO ] parmchk2 found! Using /Users/imac/anaconda3/envs/mm/bin/parmchk2
[INFO ] sander found! Using /Users/imac/anaconda3/envs/mm/bin/sander
[INFO ] Using GROMACS version > 5.x.x!
[INFO ] gmx found! Using /Users/imac/anaconda3/envs/mm/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 "name 1 GMXMMPBSA_REC\n name 13 GMXMMPBSA_LIG\n 1 | 13\n q\n" | /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md_0_100_fit.tpr
[DEBUG ] :-) GROMACS - gmx make_ndx, 2023.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /Users/imac/anaconda3/envs/mm
[DEBUG ] Working dir: /Users/imac/Desktop/Simulation/protein-ligand/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx make_ndx -n index.ndx -o _GMXMMPBSA_COM_index.ndx -f md_0_100.tpr
[DEBUG ]
[DEBUG ]
[DEBUG ] Reading structure file
[DEBUG ] Reading file md_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Reading file md_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ]
[DEBUG ] GROMACS reminds you: "What is a Unix or Linux sysadmin's favourite hangout place? Foo Bar." (Anonymous)
[DEBUG ]
[DEBUG ] Going to read 1 old index file(s)
[DEBUG ]
[DEBUG ] 0 System : 69958 atoms
[DEBUG ] 1 Protein : 6766 atoms
[DEBUG ] 2 Protein-H : 3499 atoms
[DEBUG ] 3 C-alpha : 435 atoms
[DEBUG ] 4 Backbone : 1305 atoms
[DEBUG ] 5 MainChain : 1739 atoms
[DEBUG ] 6 MainChain+Cb : 2144 atoms
[DEBUG ] 7 MainChain+H : 2146 atoms
[DEBUG ] 8 SideChain : 4620 atoms
[DEBUG ] 9 SideChain-H : 1760 atoms
[DEBUG ] 10 Prot-Masses : 6766 atoms
[DEBUG ] 11 non-Protein : 63192 atoms
[DEBUG ] 12 Other : 16 atoms
[DEBUG ] 13 LIG : 16 atoms
[DEBUG ] 14 NA : 11 atoms
[DEBUG ] 15 Water : 63165 atoms
[DEBUG ] 16 SOL : 63165 atoms
[DEBUG ] 17 non-Water : 6793 atoms
[DEBUG ] 18 Ion : 11 atoms
[DEBUG ] 19 Water_and_ions : 63176 atoms
[DEBUG ] 20 Protein_LIG : 6782 atoms
[DEBUG ] 21 LIG_&_!H* : 10 atoms
[DEBUG ] 22 System_Protein_LIG_SOL_Ion: 69958 atoms
[DEBUG ] 23 System : 69958 atoms
[DEBUG ] 24 Protein : 6766 atoms
[DEBUG ] 25 LIG : 16 atoms
[DEBUG ] 26 SOL : 63165 atoms
[DEBUG ] 27 Ion : 11 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: 6766 16 -> 6782
[DEBUG ]
[DEBUG ] >
[INFO ] Normal Complex: Saving group Protein_LIG (1_13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb
[DEBUG ] Running command: echo "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx trjconv -f md_0_100_fit.xtc -s md_0_100.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /Users/imac/anaconda3/envs/mm
[DEBUG ] Working dir: /Users/imac/Desktop/Simulation/protein-ligand/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_0_100_fit.xtc -s md_0_100_fit.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_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Reading file md_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Group 0 ( System) has 69958 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 6766 elements
[DEBUG ] Group 2 ( Protein-H) has 3499 elements
[DEBUG ] Group 3 ( C-alpha) has 435 elements
[DEBUG ] Group 4 ( Backbone) has 1305 elements
[DEBUG ] Group 5 ( MainChain) has 1739 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 2144 elements
[DEBUG ] Group 7 ( MainChain+H) has 2146 elements
[DEBUG ] Group 8 ( SideChain) has 4620 elements
[DEBUG ] Group 9 ( SideChain-H) has 1760 elements
[DEBUG ] Group 10 ( Prot-Masses) has 6766 elements
[DEBUG ] Group 11 ( non-Protein) has 63192 elements
[DEBUG ] Group 12 ( Other) has 16 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 16 elements
[DEBUG ] Group 14 ( NA) has 11 elements
[DEBUG ] Group 15 ( Water) has 63165 elements
[DEBUG ] Group 16 ( SOL) has 63165 elements
[DEBUG ] Group 17 ( non-Water) has 6793 elements
[DEBUG ] Group 18 ( Ion) has 11 elements
[DEBUG ] Group 19 ( Water_and_ions) has 63176 elements
[DEBUG ] Group 20 ( Protein_LIG) has 6782 elements
[DEBUG ] Group 21 ( LIG_&_!H*) has 10 elements
[DEBUG ] Group 22 (System_Protein_LIG_SOL_Ion) has 69958 elements
[DEBUG ] Group 23 ( System) has 69958 elements
[DEBUG ] Group 24 ( Protein) has 6766 elements
[DEBUG ] Group 25 ( LIG) has 16 elements
[DEBUG ] Group 26 ( SOL) has 63165 elements
[DEBUG ] Group 27 ( Ion) has 11 elements
[DEBUG ] Group 28 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6782 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_100_fit.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: "What is a Unix or Linux sysadmin's favourite hangout place? Foo Bar." (Anonymous)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 28: 'GMXMMPBSA_REC_GMXMMPBSA_LIG'
[INFO ] No receptor structure file was defined. Using ST approach...
[INFO ] Using receptor structure from complex to generate AMBER topology
[INFO ] Normal Receptor: Saving group Protein (1) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_REC.pdb
[DEBUG ] Running command: echo "1"| /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx trjconv -f md_0_100_fit.xtc -s md_0_100.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /Users/imac/anaconda3/envs/mm
[DEBUG ] Working dir: /Users/imac/Desktop/Simulation/protein-ligand/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_0_100_fit.xtc -s md_0_100.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_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Reading file md_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Group 0 ( System) has 69958 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 6766 elements
[DEBUG ] Group 2 ( Protein-H) has 3499 elements
[DEBUG ] Group 3 ( C-alpha) has 435 elements
[DEBUG ] Group 4 ( Backbone) has 1305 elements
[DEBUG ] Group 5 ( MainChain) has 1739 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 2144 elements
[DEBUG ] Group 7 ( MainChain+H) has 2146 elements
[DEBUG ] Group 8 ( SideChain) has 4620 elements
[DEBUG ] Group 9 ( SideChain-H) has 1760 elements
[DEBUG ] Group 10 ( Prot-Masses) has 6766 elements
[DEBUG ] Group 11 ( non-Protein) has 63192 elements
[DEBUG ] Group 12 ( Other) has 16 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 16 elements
[DEBUG ] Group 14 ( NA) has 11 elements
[DEBUG ] Group 15 ( Water) has 63165 elements
[DEBUG ] Group 16 ( SOL) has 63165 elements
[DEBUG ] Group 17 ( non-Water) has 6793 elements
[DEBUG ] Group 18 ( Ion) has 11 elements
[DEBUG ] Group 19 ( Water_and_ions) has 63176 elements
[DEBUG ] Group 20 ( Protein_LIG) has 6782 elements
[DEBUG ] Group 21 ( LIG_&_!H*) has 10 elements
[DEBUG ] Group 22 (System_Protein_LIG_SOL_Ion) has 69958 elements
[DEBUG ] Group 23 ( System) has 69958 elements
[DEBUG ] Group 24 ( Protein) has 6766 elements
[DEBUG ] Group 25 ( LIG) has 16 elements
[DEBUG ] Group 26 ( SOL) has 63165 elements
[DEBUG ] Group 27 ( Ion) has 11 elements
[DEBUG ] Group 28 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6782 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_100_fit.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: "What is a Unix or Linux sysadmin's favourite hangout place? Foo Bar." (Anonymous)
[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 LIG (13) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[DEBUG ] Running command: echo "13"| /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx trjconv -f md_0_100_fit.xtc -s md_0_100.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0
[DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /Users/imac/anaconda3/envs/mm
[DEBUG ] Working dir: /Users/imac/Desktop/Simulation/protein-ligand/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_0_100_fit.xtc -s md_0_100.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_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Reading file md_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Group 0 ( System) has 69958 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 6766 elements
[DEBUG ] Group 2 ( Protein-H) has 3499 elements
[DEBUG ] Group 3 ( C-alpha) has 435 elements
[DEBUG ] Group 4 ( Backbone) has 1305 elements
[DEBUG ] Group 5 ( MainChain) has 1739 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 2144 elements
[DEBUG ] Group 7 ( MainChain+H) has 2146 elements
[DEBUG ] Group 8 ( SideChain) has 4620 elements
[DEBUG ] Group 9 ( SideChain-H) has 1760 elements
[DEBUG ] Group 10 ( Prot-Masses) has 6766 elements
[DEBUG ] Group 11 ( non-Protein) has 63192 elements
[DEBUG ] Group 12 ( Other) has 16 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 16 elements
[DEBUG ] Group 14 ( NA) has 11 elements
[DEBUG ] Group 15 ( Water) has 63165 elements
[DEBUG ] Group 16 ( SOL) has 63165 elements
[DEBUG ] Group 17 ( non-Water) has 6793 elements
[DEBUG ] Group 18 ( Ion) has 11 elements
[DEBUG ] Group 19 ( Water_and_ions) has 63176 elements
[DEBUG ] Group 20 ( Protein_LIG) has 6782 elements
[DEBUG ] Group 21 ( LIG_&_!H*) has 10 elements
[DEBUG ] Group 22 (System_Protein_LIG_SOL_Ion) has 69958 elements
[DEBUG ] Group 23 ( System) has 69958 elements
[DEBUG ] Group 24 ( Protein) has 6766 elements
[DEBUG ] Group 25 ( LIG) has 16 elements
[DEBUG ] Group 26 ( SOL) has 63165 elements
[DEBUG ] Group 27 ( Ion) has 11 elements
[DEBUG ] Group 28 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6782 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_100_fit.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: "What is a Unix or Linux sysadmin's favourite hangout place? Foo Bar." (Anonymous)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 13: 'GMXMMPBSA_LIG'
[INFO ] Checking the structures consistency...
[INFO ]
[INFO ] Using topology conversion. Setting radiopt = 0...
[INFO ] Building Normal Complex Amber topology...
[INFO ] Detected CHARMM force field topology format...
[INFO ] Assigning PBRadii mbondi2 to Complex...
[INFO ] Writing Normal Complex AMBER topology...
[INFO ] No Receptor topology file was defined. Using ST approach...
[INFO ] Building AMBER Receptor topology from Complex...
[INFO ] Assigning PBRadii mbondi2 to Receptor...
[INFO ] Writing Normal Receptor AMBER topology...
[INFO ] No Ligand topology file was defined. Using ST approach...
[INFO ] Building AMBER Ligand topology from Complex...
[INFO ] Assigning PBRadii mbondi2 to Ligand...
[INFO ] Writing Normal Ligand AMBER topology...
[INFO ] Cleaning normal complex trajectories...
[DEBUG ] Running command: echo "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx trjconv -f md_0_100_fit.xtc -s md_0_100.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx
[DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-:
[DEBUG ]
[DEBUG ] Executable: /Users/imac/anaconda3/envs/mm/bin.AVX2_256/gmx
[DEBUG ] Data prefix: /Users/imac/anaconda3/envs/mm
[DEBUG ] Working dir: /Users/imac/Desktop/Simulation/protein-ligand/mmpbsa
[DEBUG ] Command line:
[DEBUG ] gmx trjconv -f md_0_100_fit.xtc -s md_0_100.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_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Reading file md_0_100.tpr, VERSION 2019.6 (single precision)
[DEBUG ] Group 0 ( System) has 69958 elements
[DEBUG ] Group 1 ( GMXMMPBSA_REC) has 6766 elements
[DEBUG ] Group 2 ( Protein-H) has 3499 elements
[DEBUG ] Group 3 ( C-alpha) has 435 elements
[DEBUG ] Group 4 ( Backbone) has 1305 elements
[DEBUG ] Group 5 ( MainChain) has 1739 elements
[DEBUG ] Group 6 ( MainChain+Cb) has 2144 elements
[DEBUG ] Group 7 ( MainChain+H) has 2146 elements
[DEBUG ] Group 8 ( SideChain) has 4620 elements
[DEBUG ] Group 9 ( SideChain-H) has 1760 elements
[DEBUG ] Group 10 ( Prot-Masses) has 6766 elements
[DEBUG ] Group 11 ( non-Protein) has 63192 elements
[DEBUG ] Group 12 ( Other) has 16 elements
[DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 16 elements
[DEBUG ] Group 14 ( NA) has 11 elements
[DEBUG ] Group 15 ( Water) has 63165 elements
[DEBUG ] Group 16 ( SOL) has 63165 elements
[DEBUG ] Group 17 ( non-Water) has 6793 elements
[DEBUG ] Group 18 ( Ion) has 11 elements
[DEBUG ] Group 19 ( Water_and_ions) has 63176 elements
[DEBUG ] Group 20 ( Protein_LIG) has 6782 elements
[DEBUG ] Group 21 ( LIG_&_!H*) has 10 elements
[DEBUG ] Group 22 (System_Protein_LIG_SOL_Ion) has 69958 elements
[DEBUG ] Group 23 ( System) has 69958 elements
[DEBUG ] Group 24 ( Protein) has 6766 elements
[DEBUG ] Group 25 ( LIG) has 16 elements
[DEBUG ] Group 26 ( SOL) has 63165 elements
[DEBUG ] Group 27 ( Ion) has 11 elements
[DEBUG ] Group 28 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 6782 elements
[DEBUG ] Select a group:
Reading frame 0 time 0.000
[DEBUG ] Precision of md_0_100_fit.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
Reading frame 600 time 60000.000 -> frame 599 time 59900.000
Reading frame 700 time 70000.000 -> frame 699 time 69900.000
Reading frame 800 time 80000.000 -> frame 799 time 79900.000
Reading frame 900 time 90000.000 -> frame 899 time 89900.000
Reading frame 1000 time 100000.000 -> frame 999 time 99900.000
Last frame 1000 time 100000.000
[DEBUG ] Last written: frame 1000 time 100000.000
[DEBUG ]
[DEBUG ]
[DEBUG ] GROMACS reminds you: "What do you want out of life?" (Jack Kerouac, On The Road)
[DEBUG ]
[DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility.
[DEBUG ] Select group for output
[DEBUG ] Selected 28: '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 ] 100 frames were processed by cpptraj for use in calculation.
[INFO ] Starting calculations in 1 CPUs...
[INFO ] Running calculations on normal system...
[INFO ] Beginning GB calculations with /Users/imac/anaconda3/envs/mm/bin/sander
[INFO ] calculating complex contribution...
[INFO ] calculating receptor contribution...
[INFO ] calculating ligand contribution...
[INFO ] Parsing results to output files...
[INFO ] Timing:
[INFO ] Total GROMACS setup time: 0.283 min.
[INFO ] Total AMBER setup time: 0.023 min.
[INFO ] Creating trajectories with cpptraj: 0.020 min.
[INFO ] Total calculation time: 10.680 min.
[INFO ] Total GB calculation time: 10.617 min.
[INFO ] Statistics calculation & output writing: 0.001 min.
[INFO ] Total time taken: 11.007 min.
[INFO ]
Finalizing gmx_MMPBSA: [ERROR ] = 0; [WARNING] = 0
Check the gmx_MMPBSA.log file for more details...
[INFO ]
Thank you for using gmx_MMPBSA. Please consider supporting gmx_MMPBSA by citing our publication:
Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E.
gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS.
J Chem Theory Comput., 2021, 17 (10):6281-6291. Epub 2021 Sep 29. PMID: 34586825.
https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645
Also consider citing MMPBSA.py:
Miller III, B. R., McGee Jr., T. D., Swails, J. M. Homeyer, N. Gohlke, H. and Roitberg, A. E.
MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
J. Chem. Theory Comput., 2012, 8 (9) pp 3314-3321
[INFO ] Opening gmx_MMPBSA_ana to analyze results...
[INFO ] Finalized...