VMD-L Mailing List

From: dalpizar_at_fbio.uh.cu
Date: Tue Jul 17 2018 - 15:05:07 CDT

Dear VMD expert

Im trying to parametrize a molecule in the fftk from VMD, I first use
the CHARMM-GUI web server to obtain the inputs to use in NAMD but some
parameters show high penalties, so I use this files obtained from this
server to parametrize this When I carried out all the optimizations they
run without problems except in the Bonded_Opt tab, here the program
guessed correctly all the bonds and angles, but when I put Run
Optimization the program return to me this issue:

Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID:
v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
Warning> Randomization of stack pointer is turned on in kernel, thread
migration may not work! Run 'echo 0 >
/proc/sys/kernel/randomize_va_space' as root to disable it, or try run
with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.10 for Linux-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. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60601 for multicore-linux64-iccstatic
Info: Built Tue Dec 9 15:34:29 CST 2014 by jim on despina.ks.uiuc.edu
Info: 1 NAMD 2.10 Linux-x86_64-multicore 1 GenTox dalpizar
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00114894
s
Info: 43.375 MB of memory in use based on /proc/self/stat
Info: Configuration file is min-bondangles.conf
Info: Working in the current directory
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore
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 1531322508
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/Anillo_A_Geom_Opt.pdb
Info: STRUCTURE FILE
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/ligandrm.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/lig.prm
Info: PARAMETERS OPTTEMP.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS

Warning: DUPLICATE BOND ENTRY FOR CG25C1-CG3C51
PREVIOUS VALUES k=300 x0=1.53
    USING VALUES k=399.518 x0=1.5013

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG3C51-CG3C51
PREVIOUS VALUES k=52 theta0=106 k_ub=0 r_ub=0
    USING VALUES k=299.995 theta0=99.8816 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG2DC3-CG25C1-CG3C51
PREVIOUS VALUES k=40 theta0=130 k_ub=0 r_ub=0
    USING VALUES k=83.858 theta0=130.625 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG2R53-CG25C1-CG3C51
PREVIOUS VALUES k=115 theta0=109 k_ub=0 r_ub=0
    USING VALUES k=299.995 theta0=107.19 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG2R53-OG3C51
PREVIOUS VALUES k=65.5 theta0=105 k_ub=0 r_ub=0
    USING VALUES k=299.995 theta0=107.925 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG3C51-HGA1
PREVIOUS VALUES k=52 theta0=112.6 k_ub=0 r_ub=0
    USING VALUES k=57.4288 theta0=112.227 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG3C51-CG331
PREVIOUS VALUES k=62 theta0=103 k_ub=0 r_ub=0
    USING VALUES k=87.5439 theta0=110.579 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG2R53-OG3C51-CG3C51
PREVIOUS VALUES k=90 theta0=107.1 k_ub=0 r_ub=0
    USING VALUES k=267.778 theta0=109.392 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 2 BONDS
Info: 14 ANGLES
Info: 24 DIHEDRAL
Info: 1 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51
[0] Stack Traceback:
   [0:0] CmiAbort+0x5f [0xe8725f]
   [0:1] _Z8NAMD_diePKc+0x62 [0x663b9a]
   [0:2] _ZN10Parameters16assign_vdw_indexEPcP14atom_constants+0x316
[0xc0bcf4]
   [0:3] _ZN8Molecule10read_atomsEP8_IO_FILEP10Parameters+0xff7
[0xbb3269]
   [0:4] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x332 [0xbb10ca]
   [0:5]
_ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
[0xbb0cd1]
   [0:6] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
[0xbb5bca]
   [0:7] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
   [0:8] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
   [0:9] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e [0xc79ed2]
   [0:10] TclInvokeStringCommand+0x88 [0xecef58]
   [0:11] [0xed1a70]
   [0:12] [0xed2e56]
   [0:13] Tcl_EvalEx+0x16 [0xed3636]
   [0:14] Tcl_FSEvalFileEx+0x151 [0xf35441]
   [0:15] Tcl_EvalFile+0x2e [0xf355fe]
   [0:16] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
   [0:17] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
   [0:18] main+0x3a [0x6684c2]
   [0:19] __libc_start_main+0xf0 [0x7f143f3ef830]
   [0:20] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
[0] Stack Traceback:
   [0:0] [0xe88055]
   [0:1] CmiAbort+0x9d [0xe8729d]
   [0:2] _Z8NAMD_diePKc+0x62 [0x663b9a]
   [0:3] _ZN10Parameters16assign_vdw_indexEPcP14atom_constants+0x316
[0xc0bcf4]
   [0:4] _ZN8Molecule10read_atomsEP8_IO_FILEP10Parameters+0xff7
[0xbb3269]
   [0:5] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x332 [0xbb10ca]
   [0:6]
_ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
[0xbb0cd1]
   [0:7] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
[0xbb5bca]
   [0:8] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
   [0:9] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
   [0:10] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e
[0xc79ed2]
   [0:11] TclInvokeStringCommand+0x88 [0xecef58]
   [0:12] [0xed1a70]
   [0:13] [0xed2e56]
   [0:14] Tcl_EvalEx+0x16 [0xed3636]
   [0:15] Tcl_FSEvalFileEx+0x151 [0xf35441]
   [0:16] Tcl_EvalFile+0x2e [0xf355fe]
   [0:17] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
   [0:18] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
   [0:19] main+0x3a [0x6684c2]
   [0:20] __libc_start_main+0xf0 [0x7f143f3ef830]
   [0:21] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51

Charm++ fatal error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51

Charm++: standalone mode (not using charmrun)
Converse/Charm++ Commit ID:
v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-Dec-08-28969
Warning> Randomization of stack pointer is turned on in kernel, thread
migration may not work! Run 'echo 0 >
/proc/sys/kernel/randomize_va_space' as root to disable it, or try run
with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (8-way SMP).
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.10 for Linux-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. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 60601 for multicore-linux64-iccstatic
Info: Built Tue Dec 9 15:34:29 CST 2014 by jim on despina.ks.uiuc.edu
Info: 1 NAMD 2.10 Linux-x86_64-multicore 1 GenTox dalpizar
Info: Running on 1 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00114894
s
Info: 43.375 MB of memory in use based on /proc/self/stat
Info: Configuration file is min-bondangles.conf
Info: Working in the current directory
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore
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 1531322508
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/Anillo_A_Geom_Opt.pdb
Info: STRUCTURE FILE
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/ligandrm.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/lig.prm
Info: PARAMETERS OPTTEMP.par
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS

Warning: DUPLICATE BOND ENTRY FOR CG25C1-CG3C51
PREVIOUS VALUES k=300 x0=1.53
    USING VALUES k=399.518 x0=1.5013

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG3C51-CG3C51
PREVIOUS VALUES k=52 theta0=106 k_ub=0 r_ub=0
    USING VALUES k=299.995 theta0=99.8816 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG2DC3-CG25C1-CG3C51
PREVIOUS VALUES k=40 theta0=130 k_ub=0 r_ub=0
    USING VALUES k=83.858 theta0=130.625 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG2R53-CG25C1-CG3C51
PREVIOUS VALUES k=115 theta0=109 k_ub=0 r_ub=0
    USING VALUES k=299.995 theta0=107.19 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG2R53-OG3C51
PREVIOUS VALUES k=65.5 theta0=105 k_ub=0 r_ub=0
    USING VALUES k=299.995 theta0=107.925 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG3C51-HGA1
PREVIOUS VALUES k=52 theta0=112.6 k_ub=0 r_ub=0
    USING VALUES k=57.4288 theta0=112.227 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG25C1-CG3C51-CG331
PREVIOUS VALUES k=62 theta0=103 k_ub=0 r_ub=0
    USING VALUES k=87.5439 theta0=110.579 k_ub=0 r_ub=0

Warning: DUPLICATE ANGLE ENTRY FOR CG2R53-OG3C51-CG3C51
PREVIOUS VALUES k=90 theta0=107.1 k_ub=0 r_ub=0
    USING VALUES k=267.778 theta0=109.392 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 2 BONDS
Info: 14 ANGLES
Info: 24 DIHEDRAL
Info: 1 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 0 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51
[0] Stack Traceback:
   [0:0] CmiAbort+0x5f [0xe8725f]
   [0:1] _Z8NAMD_diePKc+0x62 [0x663b9a]
   [0:2] _ZN10Parameters16assign_vdw_indexEPcP14atom_constants+0x316
[0xc0bcf4]
   [0:3] _ZN8Molecule10read_atomsEP8_IO_FILEP10Parameters+0xff7
[0xbb3269]
   [0:4] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x332 [0xbb10ca]
   [0:5]
_ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
[0xbb0cd1]
   [0:6] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
[0xbb5bca]
   [0:7] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
   [0:8] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
   [0:9] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e [0xc79ed2]
   [0:10] TclInvokeStringCommand+0x88 [0xecef58]
   [0:11] [0xed1a70]
   [0:12] [0xed2e56]
   [0:13] Tcl_EvalEx+0x16 [0xed3636]
   [0:14] Tcl_FSEvalFileEx+0x151 [0xf35441]
   [0:15] Tcl_EvalFile+0x2e [0xf355fe]
   [0:16] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
   [0:17] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
   [0:18] main+0x3a [0x6684c2]
   [0:19] __libc_start_main+0xf0 [0x7f143f3ef830]
   [0:20] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
[0] Stack Traceback:
   [0:0] [0xe88055]
   [0:1] CmiAbort+0x9d [0xe8729d]
   [0:2] _Z8NAMD_diePKc+0x62 [0x663b9a]
   [0:3] _ZN10Parameters16assign_vdw_indexEPcP14atom_constants+0x316
[0xc0bcf4]
   [0:4] _ZN8Molecule10read_atomsEP8_IO_FILEP10Parameters+0xff7
[0xbb3269]
   [0:5] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x332 [0xbb10ca]
   [0:6]
_ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x113
[0xbb0cd1]
   [0:7] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6
[0xbb5bca]
   [0:8] _ZN9NamdState14configListInitEP10ConfigList+0x8b3 [0xbe651f]
   [0:9] _ZN9ScriptTcl9initcheckEv+0xb0 [0xc7e9d0]
   [0:10] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x3e
[0xc79ed2]
   [0:11] TclInvokeStringCommand+0x88 [0xecef58]
   [0:12] [0xed1a70]
   [0:13] [0xed2e56]
   [0:14] Tcl_EvalEx+0x16 [0xed3636]
   [0:15] Tcl_FSEvalFileEx+0x151 [0xf35441]
   [0:16] Tcl_EvalFile+0x2e [0xf355fe]
   [0:17] _ZN9ScriptTcl4loadEPc+0x10 [0xc78060]
   [0:18] _Z18after_backend_initiPPc+0x3e5 [0x6688dd]
   [0:19] main+0x3a [0x6684c2]
   [0:20] __libc_start_main+0xf0 [0x7f143f3ef830]
   [0:21] _ZNSt8ios_base4InitD1Ev+0x4a [0x5d7a8a]
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51

Charm++ fatal error:
FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51

     while executing
"::exec
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/namd2
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 $::ForceFieldToolKit::Configuration::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] $scale"
     (procedure "::Optimize::Opt2::handle" line 91)
     invoked from within
"$opt initsimplex $baInitial $scale"
     (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 325)
     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)

Since the first line say "not using charmrun", I change the NAMD Bin
file for the charmrun file and then the issue is different

unning command: min-bondangles.conf

/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/charmrun:
27: exec: min-bondangles.conf: not found
Running command: min-bondangles.conf

/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/charmrun:
27: exec: min-bondangles.conf: not found
     while executing
"::exec
/home/dalpizar/Alpizar/Programas/LINUX/NAMD_2.10_Linux-x86_64-multicore/charmrun
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 $::ForceFieldToolKit::Configuration::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] $scale"
     (procedure "::Optimize::Opt3::handle" line 91)
     invoked from within
"$opt initsimplex $baInitial $scale"
     (procedure "::ForceFieldToolKit::BondAngleOpt::optimize" line 325)
     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)

Now the issue say that "exec: min-bondangles.conf: not found" so I put
all the files that Im using in the same folder where are the namd and
charmrun executables, then I run the vmd program in this same folder to
generate here the min-bondangles.conf file and then performed the same
operations above discribed and the issues were the same.

Someone know whats the problem is?

Thanks
Daniel