Charm++: standalone mode (not using charmrun)
Charm++ warning> fences and atomic operations not available in native assembly
Converse/Charm++ Commit ID: v6.6.0-43-g2d75390-namd-charm-6.6.1-build-2014-Nov-15-29369
[0] isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.016 seconds.
Info: NAMD 2.10b2 for Win64-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. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 60600 for multicore-win64
Info: Built Sat, Nov 15, 2014 11:04:17 AM by jim on europa
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.016 s
Info: 2.72656 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is min-bondangles.conf
Info: Working in the current directory C:\Users\zoran\Desktop\fftk
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-bondangles
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       min-bondangles.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     1418041819
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         C:/Users/zoran/Desktop/fftk/opt/pdobp-opt.pdb
Info: STRUCTURE FILE         C:/Users/zoran/Desktop/fftk/opt-charges1/pdobp-charge.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             C:/Users/zoran/Desktop/fftk/pdobp-init.par
Info: PARAMETERS             OPTTEMP.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 22 BONDS
Info: 72 ANGLES
Info: 45 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 8 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 27 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG321 NG2R53 PD2 (ATOMS 1 9 17)
child process exited abnormally
Charm++: standalone mode (not using charmrun)
Charm++ warning> fences and atomic operations not available in native assembly
Converse/Charm++ Commit ID: v6.6.0-43-g2d75390-namd-charm-6.6.1-build-2014-Nov-15-29369
[0] isomalloc.c> Disabling isomalloc because mmap() does not work
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Charm++> cpu topology info is gathered in 0.016 seconds.
Info: NAMD 2.10b2 for Win64-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. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: 
Info: Based on Charm++/Converse 60600 for multicore-win64
Info: Built Sat, Nov 15, 2014 11:04:17 AM by jim on europa
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.016 s
Info: 2.72656 MB of memory in use based on GetProcessMemoryInfo
Info: Configuration file is min-bondangles.conf
Info: Working in the current directory C:\Users\zoran\Desktop\fftk
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-bondangles
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME       min-bondangles.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     1418041819
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         C:/Users/zoran/Desktop/fftk/opt/pdobp-opt.pdb
Info: STRUCTURE FILE         C:/Users/zoran/Desktop/fftk/opt-charges1/pdobp-charge.psf
Info: PARAMETER file: CHARMM format! 
Info: PARAMETERS             C:/Users/zoran/Desktop/fftk/pdobp-init.par
Info: PARAMETERS             OPTTEMP.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 22 BONDS
Info: 72 ANGLES
Info: 45 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 8 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Warning: Ignored 27 bonds with zero force constants.
Warning: Will get H-H distance in rigid H2O from H-O-H angle.
FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CG321 NG2R53 PD2 (ATOMS 1 9 17)
child process exited abnormally
    while executing
"::exec D:/NAMD_2.10b2_Win64-multicore/namd2.exe min-bondangles.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 $minName.conf"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optBondsAngles" line 68)
    invoked from within
"$function $p0list"
    (procedure "construct_initial_simplex" line 22)
    invoked from within
"construct_initial_simplex [lindex $args 0] $scale"
    (procedure "::Optimize::Opt0::handle" line 91)
    invoked from within
"$opt initsimplex $baInitial $scale"
    (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 322)
    invoked from within
"::ForceFieldToolKit::BondAngleOpt::optimize"
    (procedure "::ForceFieldToolKit::gui::baoptRunOpt" line 40)
    invoked from within
"::ForceFieldToolKit::gui::baoptRunOpt "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt invoke "
    invoked from within
".fftk_gui.hlf.nb.bondangleopt.runOpt instate {pressed !disabled} { .fftk_gui.hlf.nb.bondangleopt.runOpt state !pressed; .fftk_gui.hlf.nb.bondangleopt...."
    (command bound to event)