Valdes-Tresanco-MS
commented
2 years ago Please send me your files (.top+.itp, .tpr, .ndx, *.xtc) to try to identify what is going on.
Closed bradenkeiser closed 2 years ago
Valdes-Tresanco-MS
commented
2 years ago Please send me your files (.top+.itp, .tpr, .ndx, *.xtc) to try to identify what is going on.
Valdes-Tresanco-MS
commented
2 years ago According to the files you sent me, there are many problems that are not related to the program, but to your system.
Considering the above and without going much deeper (we try not to go into too much detail because of confidentiality issues and author conflicts, although none of us work in the protein-ligand field), I performed the calculation. As you indicate, GB seems to work without problems. I also tried PB without including the decomposition and it works correctly.
[INFO ] Running calculations on normal system...
[INFO ] Beginning PB calculations with /home/mario/programs/miniconda3/envs/gmx_MMPBSA/bin/sander
[INFO ] calculating complex contribution...
100%|##########| 100/100 [elapsed: 04:37 remaining: 00:00]
[INFO ] calculating receptor contribution...
100%|##########| 100/100 [elapsed: 04:36 remaining: 00:00]
[INFO ] calculating ligand contribution...
100%|##########| 100/100 [elapsed: 00:04 remaining: 00:00]
[INFO ] Parsing results to output files...
[INFO ] Timing:
[INFO ] Total GROMACS setup time: 0.129 min.
[INFO ] Total AMBER setup time: 0.006 min.
[INFO ] Creating trajectories with cpptraj: 0.011 min.
[INFO ] Total calculation time: 9.293 min.
[INFO ] Total PB calculation time: 9.013 min.
[INFO ] Statistics calculation & output writing: 0.000 min.
[INFO ] Total time taken: 9.440 min.The problem is that when decomposition is included you can expect it to take much longer. In my case, as shown, each frame takes approximately 8 minutes, with an estimated time of one hour and 40 minutes for 100 frames using 6 CPUs.
[INFO ] Selected 20 residues:
R:A:GLY:16 R:A:THR:17 R:A:GLY:18 R:A:GLU:19 R:A:SER:25 R:A:GLY:26 R:A:PHE:52 R:A:TYR:84 R:A:SER:85 R:A:GLN:86
R:A:VAL:165 R:A:THR:174 R:A:THR:175 R:A:HIS:178 R:A:LEU:179 R:A:GLN:180 R:A:TYR:181 R:A:PRO:182 R:A:ARG:183 L:B:2MER:203
[WARNING] Using idecomp = 3 and dec_verbose = 2 will generate approximately 9600 items. Large print selections can demand a large amount of memory and take a significant amount of time to print!
[INFO ] Cleaning normal complex trajectories...
[INFO ] Building AMBER topologies from GROMACS files... Done.
[INFO ] Loading and checking parameter files for compatibility...
[INFO ] Preparing trajectories for simulation...
[INFO ] 100 frames were processed by cpptraj for use in calculation.
[INFO ] Running calculations on normal system...
[INFO ] Beginning PB calculations with /home/mario/programs/miniconda3/envs/gmx_MMPBSA/bin/sander
[INFO ] calculating complex contribution...
6%|6 | 6/100 [elapsed: 08:15 remaining: 1:37:49] Note that decomposition in your case is completely irrelevant since there is no ligand permanence in one place. Everything seems to work correctly, but if you want to follow more closely the progress of the calculation, you can install the test version we are working on which includes the progress bar I show below.
python -m pip install git+https://github.com/Valdes-Tresanco-MS/gmx_MMPBSA.git@progress_bar
bradenkeiser
commented
2 years ago Thank you, sir. I was also wondering if the PB was taking longer because I chose pairwise as oppose to per residue decomp. I was performing the decomp because I was anticipating some information on how to further improve future binding opportunities. I will try to include the progress bar, though we have difficulty getting these things onto the HPC server due to github blocking here. Thank you again!
Valdes-Tresanco-MS
commented
2 years ago I left calculating some more time and you are right, PB takes much longer than what I showed you. Apparently, it has a convergence problem estimating the non-polar component of the solvation. It is common that when there are disruptions in the trajectory it takes considerably longer, so make sure that your system is completely stable.
bradenkeiser
commented
2 years ago Ok. Then, I will focus on stabling this protein-ligand complex more before reusing gmx_MMPBSA. I have just entered the field, so I am getting used to the various procedures. Thanks again!
Valdes-Tresanco-MS
commented
2 years ago I understand. I think it's happened to all of us. If you have doubts, you can ask us for help, although we do not have much time, at least we will try to guide you.
Bug summary
Whenever I run gmx_MMPBSA with PB, there is an endless loop of "Calculating complex contribution..." regardless of endframe count. I've tried 3000, 940, and 20 to no avail. I've let it run for 14 hours on 3000 frames and for 5 hours on 20 frames.
The calculations go through fine when I omit pb and perform only GBSA and decomp (as opposed to PBSA and decomp).
Terminal output
gmx_MMPBSA.log
[INFO ] Starting gmx_MMPBSA v1.5.6 [DEBUG ] WDIR : /userhome/braden/programs/cut1/openmmtest/mutants/v165t/pbsa2 [DEBUG ] AMBERHOME : /userhome/braden/software/miniconda3/envs/pbsa2 [DEBUG ] PYTHON EXE : /userhome/braden/software/miniconda3/envs/pbsa2/bin/python [DEBUG ] PYTHON VERSION: 3.9.13 | packaged by conda-forge | (main, May 27 2022, 16:56:21) [GCC 10.3.0] [DEBUG ] MPI : /userhome/braden/software/miniconda3/envs/pbsa2/bin/mpirun [DEBUG ] ParmEd : 3.4.3 [DEBUG ] OS PLATFORM : Linux-4.4.0-142-generic-x86_64-with-glibc2.27 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #168-Ubuntu SMP Wed Jan 16 21:00:45 UTC 2019 [DEBUG ] OS PROCESSOR : x86_64
[INFO ] Command-line mpirun -np 3 gmx_MMPBSA MPI -O -i mmpbsa.in -cs ../md10.tpr -cp ../topol.top -cr ../sys_start.pdb -ci ../new_index.ndx -cg 1 13 -ct ../mdfit.xtc
[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 name [DEBUG ] | startframe = 1 # First frame to analyze [DEBUG ] | endframe = 20 # 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 = 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 ] |# Decomposition namelist variables [DEBUG ] |&decomposition [DEBUG ] | idecomp = 3 # Which type of decomposition analysis to do [DEBUG ] | dec_verbose = 2 # Control energy terms are printed to the output [DEBUG ] | print_res = "within 5" # 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 /userhome/braden/software/miniconda3/envs/pbsa2/bin/cpptraj [INFO ] tleap found! Using /userhome/braden/software/miniconda3/envs/pbsa2/bin/tleap [INFO ] parmchk2 found! Using /userhome/braden/software/miniconda3/envs/pbsa2/bin/parmchk2 [INFO ] sander found! Using /userhome/braden/software/miniconda3/envs/pbsa2/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /userhome/braden/software/gromacs-22/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 | /userhome/braden/software/gromacs-22/bin/gmx make_ndx -n ../new_index.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx make_ndx, 2022 (-: [DEBUG ] [DEBUG ] Executable: /userhome/braden/software/gromacs-22/bin/gmx [DEBUG ] Data prefix: /userhome/braden/software/gromacs-22 [DEBUG ] Working dir: /userhome/braden/programs/cut1/openmmtest/mutants/v165t/pbsa2 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n ../new_index.ndx -o _GMXMMPBSA_COM_index.ndx [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Heavier-than-air flying machines are impossible." (Lord Kelvin, President of Royal Society, 1895.) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] Counted atom numbers up to 23928 in index file [DEBUG ] [DEBUG ] 0 System : 23928 atoms [DEBUG ] 1 Protein : 2850 atoms [DEBUG ] 2 Protein-H : 1446 atoms [DEBUG ] 3 C-alpha : 202 atoms [DEBUG ] 4 Backbone : 606 atoms [DEBUG ] 5 MainChain : 807 atoms [DEBUG ] 6 MainChain+Cb : 980 atoms [DEBUG ] 7 MainChain+H : 1005 atoms [DEBUG ] 8 SideChain : 1845 atoms [DEBUG ] 9 SideChain-H : 639 atoms [DEBUG ] 10 Prot-Masses : 2850 atoms [DEBUG ] 11 non-Protein : 21078 atoms [DEBUG ] 12 Other : 24 atoms [DEBUG ] 13 2MER : 21 atoms [DEBUG ] 14 CLA : 3 atoms [DEBUG ] 15 Water : 21054 atoms [DEBUG ] 16 SOL : 21054 atoms [DEBUG ] 17 non-Water : 2874 atoms [DEBUG ] 18 Protein_2MER : 2871 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: 2850 21 -> 2871 [DEBUG ] [DEBUG ] 19 GMXMMPBSA_REC_GMXMMPBSA_LIG: 2871 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 | /userhome/braden/software/gromacs-22/bin/gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022 (-: [DEBUG ] [DEBUG ] Executable: /userhome/braden/software/gromacs-22/bin/gmx [DEBUG ] Data prefix: /userhome/braden/software/gromacs-22 [DEBUG ] Working dir: /userhome/braden/programs/cut1/openmmtest/mutants/v165t/pbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 23928 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2850 elements [DEBUG ] Group 2 ( Protein-H) has 1446 elements [DEBUG ] Group 3 ( C-alpha) has 202 elements [DEBUG ] Group 4 ( Backbone) has 606 elements [DEBUG ] Group 5 ( MainChain) has 807 elements [DEBUG ] Group 6 ( MainChain+Cb) has 980 elements [DEBUG ] Group 7 ( MainChain+H) has 1005 elements [DEBUG ] Group 8 ( SideChain) has 1845 elements [DEBUG ] Group 9 ( SideChain-H) has 639 elements [DEBUG ] Group 10 ( Prot-Masses) has 2850 elements [DEBUG ] Group 11 ( non-Protein) has 21078 elements [DEBUG ] Group 12 ( Other) has 24 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 21 elements [DEBUG ] Group 14 ( CLA) has 3 elements [DEBUG ] Group 15 ( Water) has 21054 elements [DEBUG ] Group 16 ( SOL) has 21054 elements [DEBUG ] Group 17 ( non-Water) has 2874 elements [DEBUG ] Group 18 ( Protein_2MER) has 2871 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2871 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../mdfit.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Heavier-than-air flying machines are impossible." (Lord Kelvin, President of Royal Society, 1895.) [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_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 | /userhome/braden/software/gromacs-22/bin/gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022 (-: [DEBUG ] [DEBUG ] Executable: /userhome/braden/software/gromacs-22/bin/gmx [DEBUG ] Data prefix: /userhome/braden/software/gromacs-22 [DEBUG ] Working dir: /userhome/braden/programs/cut1/openmmtest/mutants/v165t/pbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 23928 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2850 elements [DEBUG ] Group 2 ( Protein-H) has 1446 elements [DEBUG ] Group 3 ( C-alpha) has 202 elements [DEBUG ] Group 4 ( Backbone) has 606 elements [DEBUG ] Group 5 ( MainChain) has 807 elements [DEBUG ] Group 6 ( MainChain+Cb) has 980 elements [DEBUG ] Group 7 ( MainChain+H) has 1005 elements [DEBUG ] Group 8 ( SideChain) has 1845 elements [DEBUG ] Group 9 ( SideChain-H) has 639 elements [DEBUG ] Group 10 ( Prot-Masses) has 2850 elements [DEBUG ] Group 11 ( non-Protein) has 21078 elements [DEBUG ] Group 12 ( Other) has 24 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 21 elements [DEBUG ] Group 14 ( CLA) has 3 elements [DEBUG ] Group 15 ( Water) has 21054 elements [DEBUG ] Group 16 ( SOL) has 21054 elements [DEBUG ] Group 17 ( non-Water) has 2874 elements [DEBUG ] Group 18 ( Protein_2MER) has 2871 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2871 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../mdfit.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Highly organized research is guaranteed to produce nothing new." (Frank Herbert) [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 | /userhome/braden/software/gromacs-22/bin/gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2022 (-: [DEBUG ] [DEBUG ] Executable: /userhome/braden/software/gromacs-22/bin/gmx [DEBUG ] Data prefix: /userhome/braden/software/gromacs-22 [DEBUG ] Working dir: /userhome/braden/programs/cut1/openmmtest/mutants/v165t/pbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 23928 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2850 elements [DEBUG ] Group 2 ( Protein-H) has 1446 elements [DEBUG ] Group 3 ( C-alpha) has 202 elements [DEBUG ] Group 4 ( Backbone) has 606 elements [DEBUG ] Group 5 ( MainChain) has 807 elements [DEBUG ] Group 6 ( MainChain+Cb) has 980 elements [DEBUG ] Group 7 ( MainChain+H) has 1005 elements [DEBUG ] Group 8 ( SideChain) has 1845 elements [DEBUG ] Group 9 ( SideChain-H) has 639 elements [DEBUG ] Group 10 ( Prot-Masses) has 2850 elements [DEBUG ] Group 11 ( non-Protein) has 21078 elements [DEBUG ] Group 12 ( Other) has 24 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 21 elements [DEBUG ] Group 14 ( CLA) has 3 elements [DEBUG ] Group 15 ( Water) has 21054 elements [DEBUG ] Group 16 ( SOL) has 21054 elements [DEBUG ] Group 17 ( non-Water) has 2874 elements [DEBUG ] Group 18 ( Protein_2MER) has 2871 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2871 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../mdfit.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000
[DEBUG ] Dumping frame at t= 0 ps [DEBUG ] Last written: frame 0 time 0.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Highly organized research is guaranteed to produce nothing new." (Frank Herbert) [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 ] Assigning chain ID to structures files according to the reference structure... [INFO ] [INFO ] Using topology conversion. Setting radiopt = 0... [INFO ] Building Normal Complex Amber topology... [INFO ] Detected CHARMM force field topology format... [INFO ] Assigning PBRadii mbondi2 to Complex... [INFO ] Writing Normal Complex AMBER topology... [INFO ] No Receptor topology file was defined. Using ST approach... [INFO ] Building AMBER Receptor topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Receptor... [INFO ] Writing Normal Receptor AMBER topology... [INFO ] No Ligand topology file was defined. Using ST approach... [INFO ] Building AMBER Ligand topology from Complex... [INFO ] Assigning PBRadii mbondi2 to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Selecting residues by distance (5 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 15 residues: R:A:GLY:16 R:A:THR:17 R:A:GLU:19 R:A:SER:25 R:A:GLY:26 R:A:TYR:84 R:A:SER:85 R:A:VAL:165 R:A:THR:174 R:A:HIS:178 R:A:LEU:179 R:A:GLN:180 R:A:TYR:181 R:A:PRO:182 L:B:2MER:203
[WARNING] Using idecomp = 3 and dec_verbose = 2 will generate approximately 5400 items. Large print selections can demand a large amount of memory and take a significant amount of time to print! [INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo GMXMMPBSA_REC_GMXMMPBSA_LIG | /userhome/braden/software/gromacs-22/bin/gmx trjconv -f ../mdfit.xtc -s ../md10.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2022 (-: [DEBUG ] [DEBUG ] Executable: /userhome/braden/software/gromacs-22/bin/gmx [DEBUG ] Data prefix: /userhome/braden/software/gromacs-22 [DEBUG ] Working dir: /userhome/braden/programs/cut1/openmmtest/mutants/v165t/pbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../mdfit.xtc -s ../md10.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 ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../md10.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 23928 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 2850 elements [DEBUG ] Group 2 ( Protein-H) has 1446 elements [DEBUG ] Group 3 ( C-alpha) has 202 elements [DEBUG ] Group 4 ( Backbone) has 606 elements [DEBUG ] Group 5 ( MainChain) has 807 elements [DEBUG ] Group 6 ( MainChain+Cb) has 980 elements [DEBUG ] Group 7 ( MainChain+H) has 1005 elements [DEBUG ] Group 8 ( SideChain) has 1845 elements [DEBUG ] Group 9 ( SideChain-H) has 639 elements [DEBUG ] Group 10 ( Prot-Masses) has 2850 elements [DEBUG ] Group 11 ( non-Protein) has 21078 elements [DEBUG ] Group 12 ( Other) has 24 elements [DEBUG ] Group 13 ( GMXMMPBSA_LIG) has 21 elements [DEBUG ] Group 14 ( CLA) has 3 elements [DEBUG ] Group 15 ( Water) has 21054 elements [DEBUG ] Group 16 ( SOL) has 21054 elements [DEBUG ] Group 17 ( non-Water) has 2874 elements [DEBUG ] Group 18 ( Protein_2MER) has 2871 elements [DEBUG ] Group 19 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 2871 elements [DEBUG ] Select a group: Reading frame 0 time 0.000
[DEBUG ] Precision of ../mdfit.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] Reading frame 1 time 10.000 -> frame 0 time 0.000
Reading frame 2 time 20.000 -> frame 1 time 10.000
Reading frame 3 time 30.000 -> frame 2 time 20.000
Reading frame 4 time 40.000 -> frame 3 time 30.000
Reading frame 5 time 50.000 -> frame 4 time 40.000
Reading frame 6 time 60.000 -> frame 5 time 50.000
Reading frame 7 time 70.000 -> frame 6 time 60.000
Reading frame 8 time 80.000 -> frame 7 time 70.000
Reading frame 9 time 90.000 -> frame 8 time 80.000
Reading frame 10 time 100.000 -> frame 9 time 90.000
Reading frame 11 time 110.000 -> frame 10 time 100.000
Reading frame 12 time 120.000 -> frame 11 time 110.000
Reading frame 13 time 130.000 -> frame 12 time 120.000
Reading frame 14 time 140.000 -> frame 13 time 130.000
Reading frame 15 time 150.000 -> frame 14 time 140.000
Reading frame 16 time 160.000 -> frame 15 time 150.000
Reading frame 17 time 170.000 -> frame 16 time 160.000
Reading frame 18 time 180.000 -> frame 17 time 170.000
Reading frame 19 time 190.000 -> frame 18 time 180.000
Reading frame 20 time 200.000 -> frame 19 time 190.000
Reading frame 30 time 300.000 -> frame 29 time 290.000
Reading frame 40 time 400.000 -> frame 39 time 390.000
Reading frame 50 time 500.000 -> frame 49 time 490.000
Reading frame 60 time 600.000 -> frame 59 time 590.000
Reading frame 70 time 700.000 -> frame 69 time 690.000
Reading frame 80 time 800.000 -> frame 79 time 790.000
Reading frame 90 time 900.000 -> frame 89 time 890.000
Reading frame 100 time 1000.000 -> frame 99 time 990.000
Reading frame 110 time 1100.000 -> frame 109 time 1090.000
Reading frame 120 time 1200.000 -> frame 119 time 1190.000
Reading frame 130 time 1300.000 -> frame 129 time 1290.000
Reading frame 140 time 1400.000 -> frame 139 time 1390.000
Reading frame 150 time 1500.000 -> frame 149 time 1490.000
Reading frame 160 time 1600.000 -> frame 159 time 1590.000
Reading frame 170 time 1700.000 -> frame 169 time 1690.000
Reading frame 180 time 1800.000 -> frame 179 time 1790.000
Reading frame 190 time 1900.000 -> frame 189 time 1890.000
Reading frame 200 time 2000.000 -> frame 199 time 1990.000
Reading frame 300 time 3000.000 -> frame 299 time 2990.000
Reading frame 400 time 4000.000 -> frame 399 time 3990.000
Reading frame 500 time 5000.000 -> frame 499 time 4990.000
Reading frame 600 time 6000.000 -> frame 599 time 5990.000
Reading frame 700 time 7000.000 -> frame 699 time 6990.000
Reading frame 800 time 8000.000 -> frame 799 time 7990.000
Reading frame 900 time 9000.000 -> frame 899 time 8990.000
Reading frame 1000 time 10000.000 -> frame 999 time 9990.000
Reading frame 1100 time 11000.000 -> frame 1099 time 10990.000
Reading frame 1200 time 12000.000 -> frame 1199 time 11990.000
Reading frame 1300 time 13000.000 -> frame 1299 time 12990.000
Reading frame 1400 time 14000.000 -> frame 1399 time 13990.000
Reading frame 1500 time 15000.000 -> frame 1499 time 14990.000
Reading frame 1600 time 16000.000 -> frame 1599 time 15990.000
Reading frame 1700 time 17000.000 -> frame 1699 time 16990.000
Reading frame 1800 time 18000.000 -> frame 1799 time 17990.000
Reading frame 1900 time 19000.000 -> frame 1899 time 18990.000
Reading frame 2000 time 20000.000 -> frame 1999 time 19990.000
Reading frame 3000 time 30000.000 -> frame 2999 time 29990.000
Last frame 3000 time 30000.000
[DEBUG ] Last written: frame 3000 time 30000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "I was a bit of an artist, and somewhere along the way had gotten the idea that computers could be used for animation and artists, because in-betweening was so tedious... Of course, everyone thought I was nuts." (Carla Meninsky, Atari engineer) [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_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 ] 20 frames were processed by cpptraj for use in calculation. [INFO ] Running calculations on normal system... [INFO ] Beginning PB calculations with /userhome/braden/software/miniconda3/envs/pbsa2/bin/sander [INFO ] calculating complex contribution...
Operating system
Ubuntu 18.04
gmx_MMPBSA Version
1.5.6
Python version
3.9
Installation
pip