VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Tue Jul 17 2018 - 16:46:10 CDT

The error is very clear:

> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE CG3C51

You also need to include the par_all36_cgenff.prm parameter file from which this atom type is taken.

Best,
JC

> On Jul 17, 2018, at 4:05 PM, dalpizar_at_fbio.uh.cu wrote:
>
> 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
>