VMD-L Mailing List

From: JC Gumbart (gumbart_at_physics.gatech.edu)
Date: Wed Jul 18 2018 - 09:02:33 CDT

Please always copy the mailing list.

This is a more subtle error. The problem is that the NBFIX lines at the end of the cgenff par file include atom type O. The way around it is to comment out those lines UNLESS you are also using those atoms. We should really fix this in NAMD though…

Best,
JC

> On Jul 18, 2018, at 9:29 AM, dalpizar_at_fbio.uh.cu wrote:
>
> Hi JC:
>
> I already include the par_all36_cgenff.prm parameter file but now the FATAL ERROR Change:
>
> Reason: FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE O
>
> Charm++ fatal error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE O
>
> But I cant find that atom in my .prm here I upload the prm file and the par_all36_cgenff.prm parameter file that Im using
>
> Thanks
> Daniel
>
> El 2018-07-17 17:46, JC Gumbart escribió:
>> 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