Tutorial-l Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Tue May 13 2008 - 14:13:13 CDT

You should be using NAMD 2.6 with the tutorial (I assume by ubiquitin
you mean the NAMD tutorial). The tutorial should describe the
benefit of the CMAP terms in the potential energy function.

On May 13, 2008, at 5:37 AM, roberta.rostagno wrote:

> 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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