Tutorial-l Mailing List
From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Wed May 14 2008 - 15:56:24 CDT
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Well, ideally you could get your sysadmin to install NAMD 2.6.
Otherwise, removing the CMAP terms from the psf file will work. For
a more long term solution, you would have to use a topology file
without CMAP terms or remove them from the one provided. However, it
doesn't matter if they are in the parameter file used.
On May 14, 2008, at 2:00 AM, Roberta Rostagno wrote:
> the problem is that I'm not the software administrator and I can
> not upgrade NAMD. I tried to delete CMAP parameters from the
> parameter file and it worked. There is a way to use CMAP param with
> NAMD 2.5? To run dinamics with NAMD 2.5 Should I delete the CMAP
> param from all the param files?
> Thank you for your answer
> best regards
>
>
> Roberta Rostagno
> ----- Original Message ----- From: "JC Gumbart" <gumbart_at_ks.uiuc.edu>
> To: "roberta.rostagno" <roberta.rostagno_at_unimib.it>
> Cc: <tutorial-l_at_ks.uiuc.edu>
> Sent: Tuesday, May 13, 2008 9:13 PM
> Subject: Re: tutorial-l: ubuquitin tutorial-FATAL ERROR: BAD
> IMPROPER FORMAT IN CHARMM PARAMETER FILE
>
>
>> 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
>>> X-Mailer: CommuniGate Pro WebUser v5.1.10
>>> Date: Tue, 13 May 2008 12:37:07 +0200
>>> Message-ID: <web-5514727_at_backend2.pablo.unimib.it>
>>> MIME-Version: 1.0
>>> Content-Type: text/plain;charset=iso-8859-1;format="flowed"
>>> Content-Transfer-Encoding: 8bit
>>>
>>> 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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