CPPTRAJ: Trajectory Analysis. V6.17.0 (GitHub) MPI ___ ___ ___ ___ | \/ | \/ | \/ | _|_/\_|_/\_|_/\_|_ | Running on 1 processes. | Date/time: 12/19/22 19:01:08 | Available memory: 154.029 GB Reading '../input/E81A_NOH_new.top' as Amber Topology Radius Set: modified Bondi radii (mbondi) INPUT: Reading input from 'STDIN' [trajin ../input/E81A_NOH_cl_c0_300ns_off2.nc 1 224999 1] Reading '../input/E81A_NOH_cl_c0_300ns_off2.nc' as Amber NetCDF Warning: Trajectory box type is 'Truncated octahedron' but topology box type is 'None'. Warning: Setting topology box information from trajectory. [noprogress] Progress bar will not be used during Run. [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first] RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb] Saving frames 1 Writing '_MMPBSA_complex.pdb' as PDB OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart] Saving frames 1 Writing '_MMPBSA_dummycomplex.inpcrd' as Amber Restart OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-224999 nobox] Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory. Saving frames 1-224999 Writing '_MMPBSA_complex.mdcrd.0' as Amber Trajectory OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [strip :288] STRIP: Stripping atoms in mask [:288] [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb] Saving frames 1 Writing '_MMPBSA_receptor.pdb' as PDB OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart] Saving frames 1 Writing '_MMPBSA_dummyreceptor.inpcrd' as Amber Restart OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-224999 nobox] Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory. Saving frames 1-224999 Writing '_MMPBSA_receptor.mdcrd.0' as Amber Trajectory OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [unstrip] [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first] RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. [strip :1-287,289-576] STRIP: Stripping atoms in mask [:1-287,289-576] [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb] Saving frames 1 Writing '_MMPBSA_ligand.pdb' as PDB OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart] Saving frames 1 Writing '_MMPBSA_dummyligand.inpcrd' as Amber Restart OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-224999 nobox] Warning: Format not specified and extension '.0' not recognized. Defaulting to Amber Trajectory. Saving frames 1-224999 Writing '_MMPBSA_ligand.mdcrd.0' as Amber Trajectory OUTTRAJ: Writing frames associated with topology 'E81A_NOH_new.top' [unstrip] [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first] RMSD: (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), reference is first frame (!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)), mass-weighted. Best-fit RMSD will be calculated, coords will be rotated and translated. ---------- RUN BEGIN ------------------------------------------------- PARAMETER FILES (1 total): 0: E81A_NOH_new.top, 9280 atoms, 576 res, box: Truncated octahedron, 4 mol INPUT TRAJECTORIES (1 total): 0: 'E81A_NOH_cl_c0_300ns_off2.nc' is a NetCDF (NetCDF3) AMBER trajectory with coordinates, box, Parm E81A_NOH_new.top (Truncated octahedron box) (reading 224999 of 224999) Coordinate processing will occur on 224999 frames. PARALLEL INFO: Process 0 will handle 224999 frames. ..................................................... ACTION SETUP FOR PARM 'E81A_NOH_new.top' (16 actions): 0: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first] Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](9280) Reference topology: E81A_NOH_new.top Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](9280) 1: [outtraj _MMPBSA_complex.pdb onlyframes 1 nobox pdb] '_MMPBSA_complex.pdb' is a PDB file, Parm E81A_NOH_new.top no box info,: Writing frames 1 Has coordinates 2: [outtraj _MMPBSA_dummycomplex.inpcrd onlyframes 1 nobox restart] '_MMPBSA_dummycomplex.inpcrd' is an AMBER restart file, Parm E81A_NOH_new.top no box info,: Writing frames 1 Has coordinates 3: [outtraj _MMPBSA_complex.mdcrd.0 onlyframes 1-224999 nobox] '_MMPBSA_complex.mdcrd.0' is an AMBER trajectory, Parm E81A_NOH_new.top no box info,: Writing frames 1-224999 Has coordinates 4: [strip :288] Stripping 33 atoms. Stripped topology: 9247 atoms, 575 res, box: Truncated octahedron, 3 mol 5: [outtraj _MMPBSA_receptor.pdb onlyframes 1 nobox pdb] '_MMPBSA_receptor.pdb' is a PDB file, Parm E81A_NOH_new.top no box info,: Writing frames 1 Has coordinates 6: [outtraj _MMPBSA_dummyreceptor.inpcrd onlyframes 1 nobox restart] '_MMPBSA_dummyreceptor.inpcrd' is an AMBER restart file, Parm E81A_NOH_new.top no box info,: Writing frames 1 Has coordinates 7: [outtraj _MMPBSA_receptor.mdcrd.0 onlyframes 1-224999 nobox] '_MMPBSA_receptor.mdcrd.0' is an AMBER trajectory, Parm E81A_NOH_new.top no box info,: Writing frames 1-224999 Has coordinates 8: [unstrip] 9: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first] Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](9280) Reference topology: E81A_NOH_new.top Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](9280) 10: [strip :1-287,289-576] Stripping 9247 atoms. Stripped topology: 33 atoms, 1 res, box: Truncated octahedron, 1 mol 11: [outtraj _MMPBSA_ligand.pdb onlyframes 1 nobox pdb] '_MMPBSA_ligand.pdb' is a PDB file, Parm E81A_NOH_new.top no box info,: Writing frames 1 Has coordinates 12: [outtraj _MMPBSA_dummyligand.inpcrd onlyframes 1 nobox restart] '_MMPBSA_dummyligand.inpcrd' is an AMBER restart file, Parm E81A_NOH_new.top no box info,: Writing frames 1 Has coordinates 13: [outtraj _MMPBSA_ligand.mdcrd.0 onlyframes 1-224999 nobox] '_MMPBSA_ligand.mdcrd.0' is an AMBER trajectory, Parm E81A_NOH_new.top no box info,: Writing frames 1-224999 Has coordinates 14: [unstrip] 15: [rmsd !(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL) mass first] Target mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](9280) Reference topology: E81A_NOH_new.top Reference mask: [!(:WAT,Cl*,CIO,Cs+,IB,K*,Li+,MG*,Na+,Rb+,CS,RB,NA,F,CL)](9280) BEGIN PARALLEL TRAJECTORY PROCESSING: Warning: Character overflow detected writing 27840 elements to file '_MMPBSA_complex.mdcrd.0' Warning: Character overflow detected writing 27741 elements to file '_MMPBSA_receptor.mdcrd.0' Warning: Character overflow detected writing 99 elements to file '_MMPBSA_ligand.mdcrd.0' Warning: Character overflow detected writing 27840 elements to file '_MMPBSA_complex.mdcrd.0' Warning: Character overflow detected writing 27741 elements to file '_MMPBSA_receptor.mdcrd.0' Warning: Character overflow detected writing 99 elements to file '_MMPBSA_ligand.mdcrd.0' Warning: Character overflow detected writing 27840 elements to file '_MMPBSA_complex.mdcrd.0' Warning: Character overflow detected writing 27741 elements to file '_MMPBSA_receptor.mdcrd.0' Warning: Character overflow detected writing 99 elements to file '_MMPBSA_ligand.mdcrd.0' Warning: Character overflow detected writing 27840 elements to file '_MMPBSA_complex.mdcrd.0' Warning: Character overflow detected writing 27741 elements to file '_MMPBSA_receptor.mdcrd.0' Warning: Character overflow detected writing 99 elements to file '_MMPBSA_ligand.mdcrd.0' Warning: Character overflow detected writing 27840 elements to file '_MMPBSA_complex.mdcrd.0' Warning: Character overflow detected writing 27741 elements to file '_MMPBSA_receptor.mdcrd.0' Warning: Character overflow detected writing 99 elements to file '_MMPBSA_ligand.mdcrd.0' Warning: Character overflow detected writing 27840 elements to file '_MMPBSA_complex.mdcrd.0' Warning: Character overflow detected writing 27741 elements to file '_MMPBSA_receptor.mdcrd.0' Warning: Character overflow detected writing 99 elements to file '_MMPBSA_ligand.mdcrd.0' TIME: Rank 0 throughput= 44.7154 frames / second. TIME: Avg. throughput= 44.7154 frames / second. ACTION OUTPUT: OUTTRAJ: '_MMPBSA_complex.pdb': Wrote 1 frames. OUTTRAJ: '_MMPBSA_dummycomplex.inpcrd': Wrote 1 frames. OUTTRAJ: '_MMPBSA_complex.mdcrd.0': Wrote 224999 frames. OUTTRAJ: '_MMPBSA_receptor.pdb': Wrote 1 frames. OUTTRAJ: '_MMPBSA_dummyreceptor.inpcrd': Wrote 1 frames. OUTTRAJ: '_MMPBSA_receptor.mdcrd.0': Wrote 224999 frames. OUTTRAJ: '_MMPBSA_ligand.pdb': Wrote 1 frames. OUTTRAJ: '_MMPBSA_dummyligand.inpcrd': Wrote 1 frames. OUTTRAJ: '_MMPBSA_ligand.mdcrd.0': Wrote 224999 frames. TIME: Analyses took 0.0000 seconds. DATASETS (3 total): RMSD_00001 "RMSD_00001" (double, rms), size is 224999 (1.800 MB) RMSD_00002 "RMSD_00002" (double, rms), size is 224999 (1.800 MB) RMSD_00003 "RMSD_00003" (double, rms), size is 224999 (1.800 MB) Total data set memory usage is at least 5.400 MB RUN TIMING: TIME: Init : 0.0270 s ( 0.00%) TIME: Trajectory Process : 5031.8025 s (100.00%) TIME: Data Set Sync : 0.0006 s ( 0.00%) TIME: Action Post : 0.0015 s ( 0.00%) TIME: Analysis : 0.0000 s ( 0.00%) TIME: Data File Write : 0.0013 s ( 0.00%) TIME: Other : 0.0535 s ( 0.00%) TIME: Run Total 5031.8865 s ---------- RUN END --------------------------------------------------- TIME: Total execution time: 5032.0022 seconds. -------------------------------------------------------------------------------- To cite CPPTRAJ use: Daniel R. Roe and Thomas E. Cheatham, III, "PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data". J. Chem. Theory Comput., 2013, 9 (7), pp 3084-3095. Daniel R. Roe and Thomas E. Cheatham, III, "Parallelization of CPPTRAJ enables large scale analysis of molecular dynamics trajectory data". J. Comp. Chem., 2018, DOI: 10.1002/jcc25382.