Tutorial-l Mailing List

From: Roberta Rostagno (roberta.rostagno_at_unimib.it)
Date: Wed May 14 2008 - 02:00:20 CDT

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
>> **
>> ** Visit http://www.greatcircle.com/majordomo/ for more info on
>> majordomo
>> **
>
> **
> ** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
> **

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**