From: dalpizar_at_fbio.uh.cu
Date: Wed Jul 18 2018 - 10:38:52 CDT

Hi Mr. JC:

I already comment these NBFIX lines and work very well

Thanks for your time
Daniel

El 2018-07-18 10:02, JC Gumbart escribió:
> 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