From: roberta.rostagno (roberta.rostagno_at_unimib.it)
Date: Tue May 13 2008 - 05:37:07 CDT

LINE=*CMAP*
To: tutorial-l_at_ks.uiuc.edu
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Date: Tue, 13 May 2008 12:37:07 +0200
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I'm a new namd user. I'm tring to do the ubiquitin
tutorial bur I had the following error:

FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
LINE=*CMAP*

I use namd 2.5

I write you all the log file I hope this can help you

Job started at Tue May 13 11:32:34 CEST 2008
Warning: Permanently added 'node127' (RSA) to the list of
known hosts.
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.5 for Linux-i686-TCP
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 Kale et al., J. Comp. Phys. 151:283-312
(1999)
Info: in all publications reporting results obtained with
NAMD.
Info:
Info: Based on Charm++/Converse 050612 for
net-linux-tcp-icc
Info: Built Fri Sep 26 17:30:07 CDT 2003 by jim on
santiago.ks.uiuc.edu
Info: Sending usage information to NAMD developers via
UDP. Sent data is:
Info: 1 NAMD 2.5 Linux-i686-TCP 2 node101 rostagno
Info: Running on 2 processors.
Info: 1465 kB of memory in use.
Measuring processor speeds... Done.
Info: Configuration file is ubq_wb_eq.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 42 0 0
Info: PERIODIC CELL BASIS 2 0 44 0
Info: PERIODIC CELL BASIS 3 0 0 47
Info: PERIODIC CELL CENTER 31 29 17.5
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON
OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: INITIAL TEMPERATURE 310
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME ubq_wb_eq.dcd
Info: DCD FREQUENCY 250
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD
FILE
Info: XST FILENAME ubq_wb_eq.xst
Info: XST FREQUENCY 250
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME ubq_wb_eq
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ubq_wb_eq.restart
Info: RESTART FREQUENCY 500
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 0.48
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16.48
Info: ENERGY OUTPUT STEPS 100
Info: PRESSURE OUTPUT STEPS 100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 100 FS
Info: DECAY TIME IS 50 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
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 32 32 32
Info: Attempting to read FFTW data from
FFTW_NAMD_2.5_Linux-i686-TCP.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5...
6... Done.
Info: Writing FFTW data to
FFTW_NAMD_2.5_Linux-i686-TCP.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 1210671156
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../common/ubq_wb.pdb
Info: STRUCTURE FILE ../common/ubq_wb.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS
            ../common/par_all27_prot_lipid.prm
FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM PARAMETER FILE
LINE=*CMAP*
------------- Processor 0 Exiting: Called CmiAbort
------------
Reason: FATAL ERROR: BAD IMPROPER FORMAT IN CHARMM
PARAMETER FILE
LINE=*CMAP*

Stack Traceback:
   [0]
_ZN10Parameters26read_charmm_parameter_fileEPc+0x704
 [0x82023f4]
   [1]
_ZN10ParametersC2EP13SimParametersP10StringList+0x9e
 [0x8201c89]
   [2] _ZN9NamdState14configListInitEP10ConfigList+0x648
 [0x81fb628]
   [3] _ZN9ScriptTcl9initcheckEv+0x59 [0x822afa1]
   [4]
_ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e
 [0x8229212]
   [5] TclInvokeStringCommand+0x6d [0x82c27b5]
   [6] /home/mcae/NAMD_2.5_Linux-i686-TCP/namd2
[0x82f6ada]
   [7] Tcl_EvalEx+0x1cc [0x82f71ec]
   [8] Tcl_EvalFile+0x157 [0x82ef353]
   [9] _ZN9ScriptTcl3runEPc+0x1a [0x8228976]
   [10] main+0x1d2 [0x80ece52]
   [11] __libc_start_main+0xc7 [0x40069917]
   [12] sinh+0x69 [0x80eacd1]
req_handle_abort called
Fatal error on PE 0> FATAL ERROR: BAD IMPROPER FORMAT IN
CHARMM PARAMETER FILE
LINE=*CMAP*

Thank you for your help
best regards

Roberta Rostagno
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