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)