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From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Feb 14 2010 - 10:26:01 CST
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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
- Next message: Francesco Pietra: "Re: CAN'T FIND BOND PARAMETERS FOR BOND C - CPB IN PARAMETER FILES"
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