CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Feb 14 2010 - 10:26:01 CST

Hi:
I am trying to minimize a file containing heme, getting error CAN'T
FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES, as below in
full. Actually, there is no C atom in heme, and in my file it is only
for residue CO, as follows from the psf file (sorry for the incorrect
colums; unable to get plain text in gmail):

   2532 O1   154  HEME O2D  OC    -0.760000       15.9990           0
   2533 O1   155  CO   C    CM     0.021000       12.0110           0
   2534 O1   155  CO   O    OM    -0.021000       15.9990           0

I am using VMD 1.8.7 and namd2.7b2

francesco_at_tya64:~/$ charmrun $NAMD_HOME/bin/namd2 ++local +p4
++verbose min-01.conf 2&1 | tee min-01.log
[1] 3973
bash: 1: command not found
Charmrun> charmrun started...
Charmrun> adding client 0: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 1: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 2: "127.0.0.1", IP:127.0.0.1
Charmrun> adding client 3: "127.0.0.1", IP:127.0.0.1
Charmrun> Charmrun = 127.0.0.1, port = 43261
Charmrun> start 0 node program on localhost.
Charmrun> start 1 node program on localhost.
Charmrun> start 2 node program on localhost.
francesco_at_tya64:~/work_myo/md$ Charmrun> start 3 node program on localhost.
Charmrun> node programs all started
Charmrun> Waiting for 0-th client to connect.
Charmrun> Waiting for 1-th client to connect.
Charmrun> client 1 connected (IP=127.0.0.1 data_port=42210)
Charmrun> client 2 connected (IP=127.0.0.1 data_port=38956)
Charmrun> Waiting for 2-th client to connect.
Charmrun> client 3 connected (IP=127.0.0.1 data_port=35927)
Charmrun> Waiting for 3-th client to connect.
Charmrun> client 0 connected (IP=127.0.0.1 data_port=36170)
Charmrun> All clients connected.
Charmrun> IP tables sent.
Charmrun> node programs all connected
Charm++> cpu topology info is being gathered.
Charm++> Running on 1 unique compute nodes (4-way SMP).
Info: NAMD 2.7b2 for Linux-x86_64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
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 60103 for net-linux-x86_64-iccstatic
Info: Built Thu Nov 12 22:12:21 CST 2009 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD  2.7b2  Linux-x86_64  4    tya64  francesco
Info: Running on 4 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0138831 s
Info: 1.63664 MB of memory in use based on CmiMemoryUsage
Info: Found 2 config files.
Info: Configuration file is min-01.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP               2
Info: NUMBER OF STEPS        0
Info: STEPS PER CYCLE        20
Info: PERIODIC CELL BASIS 1  75 0 0
Info: PERIODIC CELL BASIS 2  0 66 0
Info: PERIODIC CELL BASIS 3  0 0 69
Info: PERIODIC CELL CENTER   14.0475 20.5256 8.67652
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY  New Load Balancers -- ASB
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: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS    20
Info: MAX PAIR PARTITIONS    8
Info: SELF PARTITION ATOMS   154
Info: SELF2 PARTITION ATOMS   154
Info: PAIR PARTITION ATOMS   318
Info: PAIR2 PARTITION ATOMS  637
Info: MIN ATOMS PER PATCH    100
Info: INITIAL TEMPERATURE    310
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC             1
Info: EXCLUDE                SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR       1
Info: DCD FILENAME           /home/francesco/work_myo/md/min-01.dcd
Info: DCD FREQUENCY          100
Info: DCD FIRST STEP         100
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME           /home/francesco/work_myo/md/min-01.xst
Info: XST FREQUENCY          100
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME        /home/francesco/work_myo/md/min-01
Info: RESTART FILENAME       /home/francesco/work_myo/md/min-01.restart
Info: RESTART FREQUENCY      100
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON           10
Info: SWITCHING OFF          12
Info: PAIRLIST DISTANCE      13.5
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                 5
Info: HYDROGEN GROUP CUTOFF  2.5
Info: PATCH DIMENSION        21
Info: ENERGY OUTPUT STEPS    50
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS    100
Info: PRESSURE OUTPUT STEPS  50
Info: FIXED ATOMS ACTIVE
Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE   310
Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: VELOCITY REASSIGNMENT FREQ  500
Info: VELOCITY REASSIGNMENT TEMP  10
Info: VELOCITY REASSIGNMENT INCR  10
Info: VELOCITY REASSIGNMENT HOLD  310
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE               1e-06
Info: PME EWALD COEFFICIENT       0.257952
Info: PME INTERPOLATION ORDER     4
Info: PME GRID DIMENSIONS         80 70 95
Info: PME MAXIMUM GRID SPACING    1.5
Info: Attempting to read FFTW data from FFTW_NAMD_2.7b2_Linux-x86_64.txt
Info: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.
Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-x86_64.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY      2
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RIGID BONDS TO HYDROGEN : ALL
Info:         ERROR TOLERANCE : 1e-08
Info:          MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED     12349
Info: USE HYDROGEN BONDS?    NO
Info: COORDINATE PDB         /home/francesco/work_myo/md/myo-CO-W-ions.pdb
Info: STRUCTURE FILE         /home/francesco/work_myo/md/myo-CO-W-ions.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
/usr/local/lib/vmd/plugins/noarch/tcl/readcharmmpar1.1/par_all27_prot_lipid_na.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS

Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2
PREVIOUS VALUES  k=130  theta0=107.5 k_ub=0 r_ub=0
  USING VALUES  k=130  theta0=107 k_ub=0 r_ub=0
Info: SUMMARY OF PARAMETERS:
Info: 307 BONDS
Info: 769 ANGLES
Info: 1254 DIHEDRAL
Info: 81 IMPROPER
Info: 6 CROSSTERM
Info: 190 VDW
Info: 0 VDW_PAIRS
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN
PARAMETER FILES

[0] Stack Traceback:
 [0] CmiAbort+0x7f  [0xab6a31]
 [1] _Z8NAMD_diePKc+0x62  [0x5093f2]
 [2] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0xfd  [0x925f75]
 [3] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x177  [0x8e4ceb]
 [4] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x35b  [0x8e1aab]
 [5] _ZN8MoleculeC9EP13SimParametersP10ParametersPcP10ConfigList+0x259
 [0x8e1661]
 [6] _ZN8MoleculeC1EP13SimParametersP10ParametersPcP10ConfigList+0x6  [0x8e56ea]
 [7] _ZN9NamdState14configListInitEP10ConfigList+0x8e2  [0x90b87c]
 [8] _ZN9ScriptTcl9initcheckEv+0x5e  [0x975570]
 [9] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x20  [0x97212c]
 [10] TclInvokeStringCommand+0x91  [0xae11d8]
 [11] TclExecuteByteCode+0x856  [0xafbabf]
 [12] Tcl_EvalObjEx+0x2bb  [0xae1beb]
 [13] Tcl_IfObjCmd+0x1be  [0xae80be]
 [14] /usr/local/namd_2.7b2/bin/namd2 [0xb17028]
 [15] Tcl_EvalEx+0x176  [0xb1766b]
 [16] Tcl_EvalFile+0x134  [0xb0f074]
 [17] _ZN9ScriptTcl4loadEPc+0x10  [0x971612]
 [18] _Z18after_backend_initiPPc+0x239  [0x50dc19]
 [19] main+0x3a  [0x50d9aa]
 [20] __libc_start_main+0xe6  [0x7f852597c1a6]
 [21] _ZNSt8ios_base4InitD1Ev+0x52  [0x508d5a]
Fatal error on PE 0> FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND
C - CPB IN PARAMETER FILES

francesco_at_tya64:~/$

Thanks for help

francesco pietra

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