Charm++> No provisioning arguments specified. Running with a single PE. Use +auto-provision to fully subscribe resources or +p1 to silence this message. Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 1 threads (PEs) Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556 CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 hosts (1 sockets x 8 cores x 1 PUs = 8-way SMP) Charm++> cpu topology info is gathered in 0.001 seconds. Info: NAMD 2.14 for MacOSX-x86_64-multicore Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: for updates, documentation, and support information. Info: Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475 Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 61002 for multicore-darwin-x86_64 Info: Built Wed Aug 5 13:07:16 CDT 2020 by jim on malaga.ks.uiuc.edu Info: 1 NAMD 2.14 MacOSX-x86_64-multicore 1 Joels-MacBook-Air.local joelsubach Info: Running on 1 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0158028 s CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification) Info: 33630.2 MB of memory in use based on ps Info: Configuration file is min-geom.conf Info: Working in the current directory /Users/joelsubach TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: MIN ATOMS PER PATCH 40 Info: INITIAL TEMPERATURE 310 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 ELECTROSTATICS SCALED BY 1 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: NO DCD TRAJECTORY OUTPUT Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME min-geom Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME min-geom.restart Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 1000 Info: SWITCHING OFF 1000 Info: PAIRLIST DISTANCE 1000 Info: PAIRLIST SHRINK RATE 0.01 Info: PAIRLIST GROW RATE 0.01 Info: PAIRLIST TRIGGER 0.3 Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 1002.5 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 100 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1697030179 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB temp.pdb Info: STRUCTURE FILE /Users/joelsubach/Desktop/PANX1_PROJECT/MODELLER_LOOP_MODEL/7dwbRCSB/7dwbRCSB_LoopModeling/BEST_MODEL/LIGANDS/Medusa_Docked_7dwb.BL04340001BEST_MODEL.pdb/GROMACS_Protein-Ligand_Complex/Step_.5/ffTK/ffTK_14C/1-sysPrep/MOL.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS /Users/joelsubach/Desktop/PANX1_PROJECT/MODELLER_LOOP_MODEL/7dwbRCSB/7dwbRCSB_LoopModeling/BEST_MODEL/LIGANDS/Medusa_Docked_7dwb.BL04340001BEST_MODEL.pdb/GROMACS_Protein-Ligand_Complex/Step_.5/ffTK/ffTK_14C/1-sysPrep/par_14C.par Info: PARAMETERS parZeroFile.par Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 21 BONDS Info: 39 ANGLES Info: 72 DIHEDRAL Info: 0 IMPROPER Info: 0 CROSSTERM Info: 15 VDW Info: 0 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Warning: Ignored 116 angles with zero force constants. FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1 OG311 (ATOMS 17 7 37 36) [Partition 0][Node 0] End of program FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1 OG311 (ATOMS 17 7 37 36) Charm++> No provisioning arguments specified. Running with a single PE. Use +auto-provision to fully subscribe resources or +p1 to silence this message. Charm++: standalone mode (not using charmrun) Charm++> Running in Multicore mode: 1 threads (PEs) Charm++> Using recursive bisection (scheme 3) for topology aware partitions Converse/Charm++ Commit ID: v6.10.2-0-g7bf00fa-namd-charm-6.10.2-build-2020-Aug-05-556 CharmLB> Load balancer assumes all CPUs are same. Charm++> Running on 1 hosts (1 sockets x 8 cores x 1 PUs = 8-way SMP) Charm++> cpu topology info is gathered in 0.001 seconds. Info: NAMD 2.14 for MacOSX-x86_64-multicore Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: for updates, documentation, and support information. Info: Info: Please cite Phillips et al., J. Chem. Phys. 153:044130 (2020) doi:10.1063/5.0014475 Info: in all publications reporting results obtained with NAMD. Info: Info: Based on Charm++/Converse 61002 for multicore-darwin-x86_64 Info: Built Wed Aug 5 13:07:16 CDT 2020 by jim on malaga.ks.uiuc.edu Info: 1 NAMD 2.14 MacOSX-x86_64-multicore 1 Joels-MacBook-Air.local joelsubach Info: Running on 1 processors, 1 nodes, 1 physical nodes. Info: CPU topology information available. Info: Charm++/Converse parallel runtime startup completed at 0.0158028 s CkLoopLib is used in SMP with simple dynamic scheduling (converse-level notification) Info: 33630.2 MB of memory in use based on ps Info: Configuration file is min-geom.conf Info: Working in the current directory /Users/joelsubach TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 Info: LOAD BALANCER Centralized Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT Info: LDB PERIOD 4000 steps Info: FIRST LDB TIMESTEP 100 Info: LAST LDB TIMESTEP -1 Info: LDB BACKGROUND SCALING 1 Info: HOM BACKGROUND SCALING 1 Info: MIN ATOMS PER PATCH 40 Info: INITIAL TEMPERATURE 310 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 ELECTROSTATICS SCALED BY 1 Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED Info: NO DCD TRAJECTORY OUTPUT Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT Info: NO VELOCITY DCD OUTPUT Info: NO FORCE DCD OUTPUT Info: OUTPUT FILENAME min-geom Info: BINARY OUTPUT FILES WILL BE USED Info: RESTART FILENAME min-geom.restart Info: RESTART FREQUENCY 1000 Info: BINARY RESTART FILES WILL BE USED Info: SWITCHING ACTIVE Info: SWITCHING ON 1000 Info: SWITCHING OFF 1000 Info: PAIRLIST DISTANCE 1000 Info: PAIRLIST SHRINK RATE 0.01 Info: PAIRLIST GROW RATE 0.01 Info: PAIRLIST TRIGGER 0.3 Info: PAIRLISTS PER CYCLE 2 Info: PAIRLISTS ENABLED Info: MARGIN 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 1002.5 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 100 Info: USING VERLET I (r-RESPA) MTS SCHEME. Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS Info: RANDOM NUMBER SEED 1697030179 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB temp.pdb Info: STRUCTURE FILE /Users/joelsubach/Desktop/PANX1_PROJECT/MODELLER_LOOP_MODEL/7dwbRCSB/7dwbRCSB_LoopModeling/BEST_MODEL/LIGANDS/Medusa_Docked_7dwb.BL04340001BEST_MODEL.pdb/GROMACS_Protein-Ligand_Complex/Step_.5/ffTK/ffTK_14C/1-sysPrep/MOL.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS /Users/joelsubach/Desktop/PANX1_PROJECT/MODELLER_LOOP_MODEL/7dwbRCSB/7dwbRCSB_LoopModeling/BEST_MODEL/LIGANDS/Medusa_Docked_7dwb.BL04340001BEST_MODEL.pdb/GROMACS_Protein-Ligand_Complex/Step_.5/ffTK/ffTK_14C/1-sysPrep/par_14C.par Info: PARAMETERS parZeroFile.par Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Info: SUMMARY OF PARAMETERS: Info: 21 BONDS Info: 39 ANGLES Info: 72 DIHEDRAL Info: 0 IMPROPER Info: 0 CROSSTERM Info: 15 VDW Info: 0 VDW_PAIRS Info: 0 NBTHOLE_PAIRS Warning: Ignored 116 angles with zero force constants. FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1 OG311 (ATOMS 17 7 37 36) [Partition 0][Node 0] End of program FATAL ERROR: UNABLE TO FIND IMPROPER PARAMETERS FOR CG2O2 CG2R51 OG2D1 OG311 (ATOMS 17 7 37 36) while executing "::exec {/Applications/NAMD_2.14_MacOSX-x86_64-multicore 2/namd2} min-geom.conf" ("eval" body line 1) invoked from within "eval ::exec [list $exec_path] [lrange $args 1 end]" (procedure "::ExecTool::exec" line 14) invoked from within "::ExecTool::exec $namdbin $name.conf" (procedure "calcMM" line 103) invoked from within "calcMM $psf $pdb $dihToFit $::ForceFieldToolKit::Configuration::namdBin $parlist" (procedure "::ForceFieldToolKit::DihOpt::optimize" line 110) invoked from within "::ForceFieldToolKit::DihOpt::optimize" (procedure "::ForceFieldToolKit::gui::doptRunOpt" line 64) invoked from within "::ForceFieldToolKit::gui::doptRunOpt " invoked from within ".fftk_gui.hlf.nb.dihopt.runOpt invoke " invoked from within ".fftk_gui.hlf.nb.dihopt.runOpt instate !disabled { .fftk_gui.hlf.nb.dihopt.runOpt invoke } " invoked from within ".fftk_gui.hlf.nb.dihopt.runOpt instate pressed { .fftk_gui.hlf.nb.dihopt.runOpt state !pressed; .fftk_gui.hlf.nb.dihopt.runOpt instate !disabled { .ff..." (command bound to event)