[Question]: Error: The complex, receptor, and ligand trajectories must be the same length.

Bug summary

Hi everyone,

I am trying to run gmx_MMPBSA on a DNA-aptamer-ligand trajectory obtained in Gromacs using the CHARMM ff. I successfully ran the calculations using the complex trajectory only, and now I want to run it using the complex + receptor trajectory as the receptor structure in the bound and unbound states is quite different (RMSD > 7A). The simulation parameters of the complex and the receptor are the same, and the only difference is the presence of the ligand.

When I run the command using the complex and receptor flags I get this error after the program generates the trajectories (COM_traj_0.xtc and REC_traj_0.xtc):

Error: The complex, receptor, and ligand trajectories must be the same length.

The trajectories are the same length (checked with gmx check) and to my understanding the program should work with only 2 trajectories provided as the ligand trajectory will be extracted from the complex. Am I missing anything?

The command I used: mpirun -np 20 gmx_MMPBSA -O -i mmpbsa.in -cs 8IF5_com.tpr -cp topol.top -ci index.ndx -cg 1 2 -ct md_fit_150_300.xtc -rs 8IF5_free.tpr -rp topol_free.top -ri groups_free.ndx -rg 1 -rt md_free_fit_150_300.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

The files I used:

https://drive.google.com/drive/folders/1yGv5WfuRzDr-BVg1-idPiB-tNir-MOcD?usp=sharing

Thank you for your help!

Alan R.

Terminal output

[INFO   ] Starting gmx_MMPBSA v1.6.1
tets
[INFO   ] Command-line
  mpirun -np 20 gmx_MMPBSA -O -i mmpbsa.in -cs ../8IF5_com.tpr -cp ../topol.top -ci ../index.ndx -cg 1 2 -ct ../md_fit_150_180.xtc -rs ../8IF5_free.tpr -rp ../topol_free.top -ri ../groups_free.ndx -rg 1 -rt ../md_free_fit_150_180.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

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

[INFO   ] Checking external programs...
[INFO   ] cpptraj found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/cpptraj
[INFO   ] tleap found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/tleap
[INFO   ] parmchk2 found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/parmchk2
[INFO   ] sander found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/sander
[INFO   ] Using GROMACS version > 5.x.x!
[INFO   ] gmx found! Using /home/keafrs/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...
[INFO   ] Normal Complex: Saving group DNA_LIG (1_2) 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 DNA (1) in _GMXMMPBSA_REC_index.ndx file as _GMXMMPBSA_REC.pdb
[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 (2) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb
[WARNING] The IE or C2 entropy method don't support the MTP approach...
[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 charmm_radii 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...
[hhnode-ib-189:129401] 19 more processes have sent help message help-mpi-btl-openib.txt / error in device init
[hhnode-ib-189:129401] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
[INFO   ] Changing the Receptor residues name format from GROMACS to AMBER...
[INFO   ] Assigning PBRadii charmm_radii 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 charmm_radii to Ligand...
[INFO   ] Writing Normal Ligand AMBER topology...
[INFO   ] Selecting residues by distance (8 Å) between receptor and ligand for decomposition analysis...
[INFO   ] Selected 19 residues:
R:A:DT:5    R:A:DG:6    R:A:DT:7    R:A:DG:9    R:A:DT:10   R:A:DC:11   R:A:DT:12   R:A:DC:13   R:A:DT:14   R:A:DC:15
R:A:DT:16   R:A:DG:17   R:A:DT:18   R:A:DG:19   R:A:DT:20   R:A:DC:21   R:A:DT:22   R:A:DC:23   L:B:LIG:27

[INFO   ] Cleaning normal complex trajectories...
[INFO   ] Cleaning normal receptor trajectories...
[INFO   ] Building AMBER topologies from GROMACS files... Done.

[INFO   ] Loading and checking parameter files for compatibility...
[INFO   ] Preparing trajectories for simulation...

[ERROR  ] MMPBSA_Error 

The complex, receptor, and ligand trajectories must be the same length. Since v1.5.0 we have simplified a few things to make the code easier to maintain. Please check the documentation

Check the gmx_MMPBSA.log file to report the problem.
  File "/home/keafrs/miniconda3/envs/gmxMMPBSA/bin/gmx_MMPBSA", line 8, in <module>
    sys.exit(gmxmmpbsa())
  File "/home/keafrs/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/app.py", line 100, in gmxmmpbsa
    app.file_setup()
  File "/home/keafrs/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/main.py", line 142, in file_setup
    GMXMMPBSA_ERROR('The complex, receptor, and ligand trajectories must be the same length. Since v1.5.0 '
  File "/home/keafrs/miniconda3/envs/gmxMMPBSA/lib/python3.10/site-packages/GMXMMPBSA/exceptions.py", line 171, in __init__
    raise exc('\n\n' + msg + '\n\nCheck the gmx_MMPBSA.log file to report the problem.')
MMPBSA_Error: 

The complex, receptor, and ligand trajectories must be the same length. Since v1.5.0 we have simplified a few things to make the code easier to maintain. Please check the documentation

Check the gmx_MMPBSA.log file to report the problem.
Error occurred on rank 0.
Exiting. All files have been retained.
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------

gmx_MMPBSA.log

[INFO ] Starting gmx_MMPBSA v1.6.1 [DEBUG ] WDIR : /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] AMBERHOME : /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] PYTHON EXE : /opt/ohpc/pub/apps/anaconda3-2024.02/bin/python [DEBUG ] PYTHON VERSION: 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0] [DEBUG ] MPI : /opt/ohpc/pub/mpi/openmpi3-gnu8/3.1.4/bin/mpirun [DEBUG ] ParmEd : 4.2.2 [DEBUG ] OS PLATFORM : Linux-3.10.0-1062.el7.x86_64-x86_64-with-glibc2.17 [DEBUG ] OS SYSTEM : Linux [DEBUG ] OS VERSION : #1 SMP Wed Aug 7 18:08:02 UTC 2019 [DEBUG ] OS PROCESSOR : x86_64

[INFO ] Command-line mpirun -np 20 gmx_MMPBSA -O -i mmpbsa.in -cs ../8IF5_com.tpr -cp ../topol.top -ci ../index.ndx -cg 1 2 -ct ../md_fit_150_180.xtc -rs ../8IF5_free.tpr -rp ../topol_free.top -ri ../groups_free.ndx -rg 1 -rt ../md_free_fit_150_180.xtc -o FINAL_RESULTS_MMPBSA.dat -eo FINAL_RESULTS_MMPBSA.csv

[DEBUG ] |Input file: [DEBUG ] |--------- [DEBUG ] |Input [DEBUG ] |Be [DEBUG ] | [DEBUG ] |# General namelist variables [DEBUG ] |&general [DEBUG ] | sys_name [DEBUG ] | startframe [DEBUG ] | endframe [DEBUG ] | interval [DEBUG ] |# forcefields [DEBUG ] | ions_parameters [DEBUG ] | PBRadii [DEBUG ] | temperature [DEBUG ] | qh_entropy [DEBUG ] | [DEBUG ] | ie_segment [DEBUG ] | c2_entropy [DEBUG ] | assign_chainID [DEBUG ] | exp_ki [DEBUG ] | full_traj [DEBUG ] | # gmx_path [DEBUG ] | keep_files [DEBUG ] | netcdf [DEBUG ] | [DEBUG ] | verbose [DEBUG ] |/ [DEBUG ] | [DEBUG ] |# [DEBUG ] |&pb [DEBUG ] | ipb [DEBUG ] | inp [DEBUG ] | sander_apbs [DEBUG ] | indi [DEBUG ] | exdi [DEBUG ] | emem [DEBUG ] | smoothopt [DEBUG ] | istrng [DEBUG ] | radiopt [DEBUG ] | prbrad [DEBUG ] | iprob [DEBUG ] | sasopt [DEBUG ] | arcres [DEBUG ] | memopt [DEBUG ] | mprob [DEBUG ] | mthick [DEBUG ] | mctrdz [DEBUG ] | poretype [DEBUG ] | npbopt [DEBUG ] | solvopt [DEBUG ] | accept [DEBUG ] | linit [DEBUG ] | fillratio [DEBUG ] | scale [DEBUG ] | nbuffer [DEBUG ] | nfocus [DEBUG ] | fscale [DEBUG ] | npbgrid [DEBUG ] | bcopt [DEBUG ] | eneopt [DEBUG ] | frcopt [DEBUG ] | scalec [DEBUG ] | cutfd [DEBUG ] | cutnb [DEBUG ] | nsnba [DEBUG ] | decompopt [DEBUG ] | use_rmin [DEBUG ] | sprob [DEBUG ] | vprob [DEBUG ] | rhow_effect [DEBUG ] | use_sav [DEBUG ] | cavity_surften [DEBUG ] | cavity_offset [DEBUG ] | maxsph [DEBUG ] | maxarcdot [DEBUG ] | npbverb [DEBUG ] |/ [DEBUG ] | [DEBUG ] |# [DEBUG ] |&decomposition [DEBUG ] | idecomp [DEBUG ] | dec_verbose [DEBUG ] | print_res [DEBUG ] | csv_format [DEBUG ] |/ [DEBUG ] | [DEBUG ] |--------- [DEBUG ] [INFO ] Checking [INFO ] Checking ----------------------------------------------------- file generated by gmx_MMPBSA (v1.6.1) careful with the variables you modify, some can have severe consequences on the results you obtain. = "8IF5" # System name = 1 # First frame to analyze = 9999999 # Last frame to analyze = 1 # Number of frames between adjacent frames analyzed = # Define the force field to build the Amber topology = 1 # Define ions parameters to build the Amber topology = 7 # Define PBRadii to build amber topology from GROMACS files = 298.15 # Temperature = 0 # Do quasi-harmonic calculation interaction_entropy = 0 # Do Interaction Entropy calculation = 25 # Trajectory segment to calculate interaction entropy = 1 # Do C2 Entropy calculation = 0 # Assign chains ID = 0.0 # Experimental Ki in nM = 0 # Print a full traj. AND the thread trajectories = "" # Force to use this path to get GROMACS executable = 2 # How many files to keep after successful completion = 0 # Use NetCDF intermediate trajectories solvated_trajectory = 1 # Define if it is necessary to cleanup the trajectories = 1 # How many energy terms to print in the final output (AMBER) Possion-Boltzmann namelist variables = 2 # Dielectric model for PB = 1 # Nonpolar solvation method = 0 # Use sander.APBS? = 1.0 # Internal dielectric constant = 80.0 # External dielectric constant = 4.0 # Membrane dielectric constant = 1 # Set up dielectric values for finite-difference grid edges that are located across the solute/solvent dielectric boundary = 0.250 # Ionic strength (M) = 0 # Use optimized radii? = 1.4 # Probe radius = 2.0 # Mobile ion probe radius (Angstroms) for ion accessible surface used to define the Stern layer = 0 # Molecular surface in PB implict model = 0.25 # The resolution (Å) to compute solvent accessible arcs = 0 # Use PB optimization for membrane = 2.7 # Membrane probe radius in Å = 40.0 # Membrane thickness = 0.0 # Distance to offset membrane in Z direction = 1 # Use exclusion region for channel proteins = 0 # Use NonLinear PB solver? = 1 # Select iterative solver = 0.001 # Sets the iteration convergence criterion (relative to the initial residue) = 1000 # Number of SCF iterations = 4.0 # Ratio between the longest dimension of the rectangular finite-difference grid and that of the solute = 2.0 # 1/scale = grid spacing for the finite difference solver (default = 1/2 Å) = 0.0 # Sets how far away (in grid units) the boundary of the finite difference grid is away from the solute surface = 2 # Electrostatic focusing calculation = 8 # Set the ratio between the coarse and fine grid spacings in an electrostatic focussing calculation = 1 # Sets how often the finite-difference grid is regenerated = 5 # Boundary condition option = 2 # Compute electrostatic energy and forces = 2 # Output for computing electrostatic forces = 0 # Option to compute reaction field energy and forces = 5.0 # Cutoff for finite-difference interactions = 0.0 # Cutoff for nonbonded interations = 1 # Sets how often atom-based pairlist is generated = 2 # Option to select different decomposition schemes when INP = 2 = 1 # The option to set up van der Waals radii = 0.557 # Solvent probe radius for SASA used to compute the dispersion term = 1.3 # Solvent probe radius for molecular volume (the volume enclosed by SASA) = 1.129 # Effective water density used in the non-polar dispersion term calculation = 1 # Use molecular volume (the volume enclosed by SASA) for cavity term calculation = 0.0378 # Surface tension = -0.5692 # Offset for nonpolar solvation calc = 400 # Approximate number of dots to represent the maximum atomic solvent accessible surface = 1500 # Number of dots used to store arc dots per atom = 0 # Option to turn on verbose mode Decomposition namelist variables = 2 # Which type of decomposition analysis to do = 2 # Control energy terms are printed to the output = "within 8" # Which residues to print decomposition data for = 1 # Write decomposition data in CSV format ----------------------------------------------------- mmpbsa.in input file... mmpbsa.in input file...Done.

[INFO ] Checking external programs... [INFO ] cpptraj found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/cpptraj [INFO ] tleap found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/tleap [INFO ] parmchk2 found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/parmchk2 [INFO ] sander found! Using /home/keafrs/miniconda3/envs/gmxMMPBSA/bin/sander [INFO ] Using GROMACS version > 5.x.x! [INFO ] gmx found! Using /home/keafrs/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 1 GMXMMPBSA_REC\n name 2 GMXMMPBSA_LIG\n 1 | 2\n q\n" | /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n ../index.ndx -o _GMXMMPBSA_COM_index.ndx -f ../8IF5_com.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n ../index.ndx -o _GMXMMPBSA_COM_index.ndx -f ../8IF5_com.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "Your Bones Got a Little Machine" (Pixies) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 System : 22492 atoms [DEBUG ] 1 DNA : 824 atoms [DEBUG ] 2 LIG : 37 atoms [DEBUG ] 3 NA : 25 atoms [DEBUG ] 4 CL : 14 atoms [DEBUG ] 5 MG : 7 atoms [DEBUG ] 6 Water : 21585 atoms [DEBUG ] 7 SOL : 21585 atoms [DEBUG ] 8 non-Water : 907 atoms [DEBUG ] 9 Ion : 46 atoms [DEBUG ] 10 Water_and_ions : 21631 atoms [DEBUG ] 11 DNA_LIG : 861 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 2 'GMXMMPBSA_LIG' [DEBUG ] Merged two groups with OR: 824 37 -> 861 [DEBUG ] [DEBUG ] > [INFO ] Normal Complex: Saving group DNA_LIG (1_2) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_COM.pdb [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f ../md_fit_150_180.xtc -s ../8IF5_com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../md_fit_150_180.xtc -s ../8IF5_com.tpr -o _GMXMMPBSA_COM.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 22492 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 824 elements [DEBUG ] Group 2 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 3 ( NA) has 25 elements [DEBUG ] Group 4 ( CL) has 14 elements [DEBUG ] Group 5 ( MG) has 7 elements [DEBUG ] Group 6 ( Water) has 21585 elements [DEBUG ] Group 7 ( SOL) has 21585 elements [DEBUG ] Group 8 ( non-Water) has 907 elements [DEBUG ] Group 9 ( Ion) has 46 elements [DEBUG ] Group 10 ( Water_and_ions) has 21631 elements [DEBUG ] Group 11 ( DNA_LIG) has 861 elements [DEBUG ] Group 12 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 861 elements [DEBUG ] Select a group: Reading frame 0 time 150000.000
[DEBUG ] Precision of ../md_fit_150_180.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 150005.000
[DEBUG ] Dumping frame at t= 150000 ps [DEBUG ] Last written: frame 0 time 150000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Your Bones Got a Little Machine" (Pixies) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 12: '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/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx make_ndx -n ../groups_free.ndx -o _GMXMMPBSA_REC_index.ndx -f ../8IF5_free.tpr [DEBUG ] :-) GROMACS - gmx make_ndx, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx make_ndx -n ../groups_free.ndx -o _GMXMMPBSA_REC_index.ndx -f ../8IF5_free.tpr [DEBUG ] [DEBUG ] [DEBUG ] Reading structure file [DEBUG ] Reading file ../8IF5_free.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_free.tpr, VERSION 2022 (single precision) [DEBUG ] [DEBUG ] GROMACS reminds you: "Your Bones Got a Little Machine" (Pixies) [DEBUG ] [DEBUG ] Going to read 1 old index file(s) [DEBUG ] [DEBUG ] 0 System : 22491 atoms [DEBUG ] 1 DNA : 824 atoms [DEBUG ] 2 NA : 25 atoms [DEBUG ] 3 CL : 14 atoms [DEBUG ] 4 MG : 7 atoms [DEBUG ] 5 Water : 21621 atoms [DEBUG ] 6 SOL : 21621 atoms [DEBUG ] 7 non-Water : 870 atoms [DEBUG ] 8 Ion : 46 atoms [DEBUG ] 9 NA : 25 atoms [DEBUG ] 10 CL : 14 atoms [DEBUG ] 11 MG : 7 atoms [DEBUG ] 12 Water_and_ions : 21667 atoms [DEBUG ] 13 DNA : 824 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 DNA (1) in _GMXMMPBSA_REC_index.ndx file as _GMXMMPBSA_REC.pdb [DEBUG ] Running command: echo -e "1"| /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f ../md_free_fit_150_180.xtc -s ../8IF5_free.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_REC_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../md_free_fit_150_180.xtc -s ../8IF5_free.tpr -o _GMXMMPBSA_REC.pdb -n _GMXMMPBSA_REC_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../8IF5_free.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_free.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 22491 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 824 elements [DEBUG ] Group 2 ( NA) has 25 elements [DEBUG ] Group 3 ( CL) has 14 elements [DEBUG ] Group 4 ( MG) has 7 elements [DEBUG ] Group 5 ( Water) has 21621 elements [DEBUG ] Group 6 ( SOL) has 21621 elements [DEBUG ] Group 7 ( non-Water) has 870 elements [DEBUG ] Group 8 ( Ion) has 46 elements [DEBUG ] Group 9 ( NA) has 25 elements [DEBUG ] Group 10 ( CL) has 14 elements [DEBUG ] Group 11 ( MG) has 7 elements [DEBUG ] Group 12 ( Water_and_ions) has 21667 elements [DEBUG ] Group 13 ( DNA) has 824 elements [DEBUG ] Select a group: Reading frame 0 time 150000.000
[DEBUG ] Precision of ../md_free_fit_150_180.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 150005.000
[DEBUG ] Dumping frame at t= 150000 ps [DEBUG ] Last written: frame 0 time 150000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Your Bones Got a Little Machine" (Pixies) [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 (2) in _GMXMMPBSA_COM_index.ndx file as _GMXMMPBSA_LIG.pdb [DEBUG ] Running command: echo -e "2"| /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f ../md_fit_150_180.xtc -s ../8IF5_com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../md_fit_150_180.xtc -s ../8IF5_com.tpr -o _GMXMMPBSA_LIG.pdb -n _GMXMMPBSA_COM_index.ndx -dump 0 [DEBUG ] [DEBUG ] Will write pdb: Protein data bank file [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 22492 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 824 elements [DEBUG ] Group 2 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 3 ( NA) has 25 elements [DEBUG ] Group 4 ( CL) has 14 elements [DEBUG ] Group 5 ( MG) has 7 elements [DEBUG ] Group 6 ( Water) has 21585 elements [DEBUG ] Group 7 ( SOL) has 21585 elements [DEBUG ] Group 8 ( non-Water) has 907 elements [DEBUG ] Group 9 ( Ion) has 46 elements [DEBUG ] Group 10 ( Water_and_ions) has 21631 elements [DEBUG ] Group 11 ( DNA_LIG) has 861 elements [DEBUG ] Group 12 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 861 elements [DEBUG ] Select a group: Reading frame 0 time 150000.000
[DEBUG ] Precision of ../md_fit_150_180.xtc is 0.001 (nm) [DEBUG ] Reading frame 1 time 150005.000
[DEBUG ] Dumping frame at t= 150000 ps [DEBUG ] Last written: frame 0 time 150000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Your Bones Got a Little Machine" (Pixies) [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' [WARNING] The IE or C2 entropy method don't support the MTP approach... [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 charmm_radii 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... [INFO ] Assigning PBRadii charmm_radii 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 charmm_radii to Ligand... [INFO ] Writing Normal Ligand AMBER topology... [INFO ] Selecting residues by distance (8 Å) between receptor and ligand for decomposition analysis... [INFO ] Selected 19 residues: R:A:DT:5 R:A:DG:6 R:A:DT:7 R:A:DG:9 R:A:DT:10 R:A:DC:11 R:A:DT:12 R:A:DC:13 R:A:DT:14 R:A:DC:15 R:A:DT:16 R:A:DG:17 R:A:DT:18 R:A:DG:19 R:A:DT:20 R:A:DC:21 R:A:DT:22 R:A:DC:23 L:B:LIG:27

[INFO ] Cleaning normal complex trajectories... [DEBUG ] Running command: echo -e "GMXMMPBSA_REC_GMXMMPBSA_LIG"| /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f ../md_fit_150_180.xtc -s ../8IF5_com.tpr -o COM_traj_0.xtc -n _GMXMMPBSA_COM_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../md_fit_150_180.xtc -s ../8IF5_com.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 ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_com.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 22492 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 824 elements [DEBUG ] Group 2 ( GMXMMPBSA_LIG) has 37 elements [DEBUG ] Group 3 ( NA) has 25 elements [DEBUG ] Group 4 ( CL) has 14 elements [DEBUG ] Group 5 ( MG) has 7 elements [DEBUG ] Group 6 ( Water) has 21585 elements [DEBUG ] Group 7 ( SOL) has 21585 elements [DEBUG ] Group 8 ( non-Water) has 907 elements [DEBUG ] Group 9 ( Ion) has 46 elements [DEBUG ] Group 10 ( Water_and_ions) has 21631 elements [DEBUG ] Group 11 ( DNA_LIG) has 861 elements [DEBUG ] Group 12 (GMXMMPBSA_REC_GMXMMPBSA_LIG) has 861 elements [DEBUG ] Select a group: Reading frame 0 time 150000.000
[DEBUG ] Precision of ../md_fit_150_180.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] Reading frame 1 time 150005.000 -> frame 0 time 150000.000

Reading frame 2 time 150010.000 -> frame 1 time 150005.000

Reading frame 3 time 150015.000 -> frame 2 time 150010.000

Reading frame 4 time 150020.000 -> frame 3 time 150015.000

Reading frame 5 time 150025.000 -> frame 4 time 150020.000

Reading frame 6 time 150030.000 -> frame 5 time 150025.000

Reading frame 7 time 150035.000 -> frame 6 time 150030.000

Reading frame 8 time 150040.000 -> frame 7 time 150035.000

Reading frame 9 time 150045.000 -> frame 8 time 150040.000

Reading frame 10 time 150050.000 -> frame 9 time 150045.000

Reading frame 11 time 150055.000 -> frame 10 time 150050.000

Reading frame 12 time 150060.000 -> frame 11 time 150055.000

Reading frame 13 time 150065.000 -> frame 12 time 150060.000

Reading frame 14 time 150070.000 -> frame 13 time 150065.000

Reading frame 15 time 150075.000 -> frame 14 time 150070.000

Reading frame 16 time 150080.000 -> frame 15 time 150075.000

Reading frame 17 time 150085.000 -> frame 16 time 150080.000

Reading frame 18 time 150090.000 -> frame 17 time 150085.000

Reading frame 19 time 150095.000 -> frame 18 time 150090.000

Reading frame 20 time 150100.000 -> frame 19 time 150095.000

Reading frame 30 time 150150.000 -> frame 29 time 150145.000

Reading frame 40 time 150200.000 -> frame 39 time 150195.000

Reading frame 50 time 150250.000 -> frame 49 time 150245.000

Reading frame 60 time 150300.000 -> frame 59 time 150295.000

Reading frame 70 time 150350.000 -> frame 69 time 150345.000

Reading frame 80 time 150400.000 -> frame 79 time 150395.000

Reading frame 90 time 150450.000 -> frame 89 time 150445.000

Reading frame 100 time 150500.000 -> frame 99 time 150495.000

Reading frame 110 time 150550.000 -> frame 109 time 150545.000

Reading frame 120 time 150600.000 -> frame 119 time 150595.000

Reading frame 130 time 150650.000 -> frame 129 time 150645.000

Reading frame 140 time 150700.000 -> frame 139 time 150695.000

Reading frame 150 time 150750.000 -> frame 149 time 150745.000

Reading frame 160 time 150800.000 -> frame 159 time 150795.000

Reading frame 170 time 150850.000 -> frame 169 time 150845.000

Reading frame 180 time 150900.000 -> frame 179 time 150895.000

Reading frame 190 time 150950.000 -> frame 189 time 150945.000

Reading frame 200 time 151000.000 -> frame 199 time 150995.000

Reading frame 300 time 151500.000 -> frame 299 time 151495.000

Reading frame 400 time 152000.000 -> frame 399 time 151995.000

Reading frame 500 time 152500.000 -> frame 499 time 152495.000

Reading frame 600 time 153000.000 -> frame 599 time 152995.000

Reading frame 700 time 153500.000 -> frame 699 time 153495.000

Reading frame 800 time 154000.000 -> frame 799 time 153995.000

Reading frame 900 time 154500.000 -> frame 899 time 154495.000

Reading frame 1000 time 155000.000 -> frame 999 time 154995.000

Reading frame 1100 time 155500.000 -> frame 1099 time 155495.000

Reading frame 1200 time 156000.000 -> frame 1199 time 155995.000

Reading frame 1300 time 156500.000 -> frame 1299 time 156495.000

Reading frame 1400 time 157000.000 -> frame 1399 time 156995.000

Reading frame 1500 time 157500.000 -> frame 1499 time 157495.000

Reading frame 1600 time 158000.000 -> frame 1599 time 157995.000

Reading frame 1700 time 158500.000 -> frame 1699 time 158495.000

Reading frame 1800 time 159000.000 -> frame 1799 time 158995.000

Reading frame 1900 time 159500.000 -> frame 1899 time 159495.000

Reading frame 2000 time 160000.000 -> frame 1999 time 159995.000

Reading frame 3000 time 165000.000 -> frame 2999 time 164995.000

Reading frame 4000 time 170000.000 -> frame 3999 time 169995.000

Reading frame 5000 time 175000.000 -> frame 4999 time 174995.000

Reading frame 6000 time 180000.000 -> frame 5999 time 179995.000

Last frame 6000 time 180000.000
[DEBUG ] Last written: frame 6000 time 180000.000 [DEBUG ] [DEBUG ] [DEBUG ] GROMACS reminds you: "Count the Bubbles In Your Hair" (The Breeders) [DEBUG ] [DEBUG ] Note that major changes are planned in future for trjconv, to improve usability and utility. [DEBUG ] Select group for output [DEBUG ] Selected 12: 'GMXMMPBSA_REC_GMXMMPBSA_LIG' [INFO ] Cleaning normal receptor trajectories... [DEBUG ] Running command: echo -e "GMXMMPBSA_REC"| /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx trjconv -f ../md_free_fit_150_180.xtc -s ../8IF5_free.tpr -o REC_traj_0.xtc -n _GMXMMPBSA_REC_index.ndx [DEBUG ] :-) GROMACS - gmx trjconv, 2023.4-conda_forge (-: [DEBUG ] [DEBUG ] Executable: /home/keafrs/miniconda3/envs/gmxMMPBSA/bin.AVX2_256/gmx [DEBUG ] Data prefix: /home/keafrs/miniconda3/envs/gmxMMPBSA [DEBUG ] Working dir: /home/keafrs/8if5/com_energy/mmpbsa/mmpbsa2 [DEBUG ] Command line: [DEBUG ] gmx trjconv -f ../md_free_fit_150_180.xtc -s ../8IF5_free.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 ../8IF5_free.tpr, VERSION 2022 (single precision) [DEBUG ] Reading file ../8IF5_free.tpr, VERSION 2022 (single precision) [DEBUG ] Group 0 ( System) has 22491 elements [DEBUG ] Group 1 ( GMXMMPBSA_REC) has 824 elements [DEBUG ] Group 2 ( NA) has 25 elements [DEBUG ] Group 3 ( CL) has 14 elements [DEBUG ] Group 4 ( MG) has 7 elements [DEBUG ] Group 5 ( Water) has 21621 elements [DEBUG ] Group 6 ( SOL) has 21621 elements [DEBUG ] Group 7 ( non-Water) has 870 elements [DEBUG ] Group 8 ( Ion) has 46 elements [DEBUG ] Group 9 ( NA) has 25 elements [DEBUG ] Group 10 ( CL) has 14 elements [DEBUG ] Group 11 ( MG) has 7 elements [DEBUG ] Group 12 ( Water_and_ions) has 21667 elements [DEBUG ] Group 13 ( DNA) has 824 elements [DEBUG ] Select a group: Reading frame 0 time 150000.000
[DEBUG ] Precision of ../md_free_fit_150_180.xtc is 0.001 (nm) [DEBUG ] Using output precision of 0.001 (nm) [DEBUG ] Reading frame 1 time 150005.000 -> frame 0 time 150000.000