From: Narasimhan LOGANATHAN (Narasimhan.Loganathan_at_etu.univ-provence.fr)
Date: Tue Jun 07 2011 - 11:15:10 CDT
Hi,
Thanks for the reply. Herewith, i aam posting the information in the log file.
And also the custom forcefield in X-plor format
#############################################
Log File
#############################################
Charm++: standalone mode (not using charmrun)
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
Charm++: scheduler running in netpoll mode.
Charm++> Running on 1 unique compute nodes (12-way SMP).
Charm++> Cpu topology info:
PE to node map: 0
Node to PE map:
Chip #0: 0
Charm++> cpu topology info is gathered in 0.000 seconds.
Info: NAMD 2.7 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 60202 for net-linux-x86_64-iccstatic
Info: Built Wed Oct 13 11:38:08 CDT 2010 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.7 Linux-x86_64 1 nanpc45.in2p3.fr accelrys
Info: Running on 1 processors.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.00228715 s
Info: 1.49471 MB of memory in use based on CmiMemoryUsage
Info: Configuration file is water.conf
TCL: Suspending until startup complete.
ERROR: 'exclude' is a required configuration option
ERROR: exclude defines: Electrostatic and VDW exclusion policy
ERROR: The following variables were set in the
ERROR: configuration file but are NOT VALID
ERROR: if{0}
FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
[0] Stack Traceback:
[0:0] CmiAbort+0x7b [0xb3ecb1]
[0:1] _Z8NAMD_diePKc+0x62 [0x520802]
[0:2] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73 [0xa0f199]
[0:3] _ZN9NamdState14configListInitEP10ConfigList+0x3d9 [0x978d37]
[0:4] _ZN9ScriptTcl9initcheckEv+0x5e [0x9e9a9c]
[0:5] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x20 [0x9e6364]
[0:6] TclInvokeStringCommand+0x91 [0xb6ca38]
[0:7] namd2 [0xba2888]
[0:8] Tcl_EvalEx+0x176 [0xba2ecb]
[0:9] Tcl_EvalFile+0x134 [0xb9a8d4]
[0:10] _ZN9ScriptTcl3runEPc+0x14 [0x9e5b82]
[0:11] _Z18after_backend_initiPPc+0x22b [0x525053]
[0:12] main+0x3a [0x524df2]
[0:13] __libc_start_main+0xf4 [0x3dc541d994]
[0:14] _ZNSt8ios_base4InitD1Ev+0x4a [0x5200fa]
[0] Stack Traceback:
[0:0] namd2 [0xb3f86d]
[0:1] CmiAbort+0xb9 [0xb3ecef]
[0:2] _Z8NAMD_diePKc+0x62 [0x520802]
[0:3] _ZN13SimParameters22initialize_config_dataEP10ConfigListRPc+0x73 [0xa0f199]
[0:4] _ZN9NamdState14configListInitEP10ConfigList+0x3d9 [0x978d37]
[0:5] _ZN9ScriptTcl9initcheckEv+0x5e [0x9e9a9c]
[0:6] _ZN9ScriptTcl7Tcl_runEPvP10Tcl_InterpiPPc+0x20 [0x9e6364]
[0:7] TclInvokeStringCommand+0x91 [0xb6ca38]
[0:8] namd2 [0xba2888]
[0:9] Tcl_EvalEx+0x176 [0xba2ecb]
[0:10] Tcl_EvalFile+0x134 [0xb9a8d4]
[0:11] _ZN9ScriptTcl3runEPc+0x14 [0x9e5b82]
[0:12] _Z18after_backend_initiPPc+0x22b [0x525053]
[0:13] main+0x3a [0x524df2]
[0:14] __libc_start_main+0xf4 [0x3dc541d994]
[0:15] _ZNSt8ios_base4InitD1Ev+0x4a [0x5200fa]
#################################
custom Forcefield X-plor Format
#################################
REMARKS - parameter file ClayFF -
REMARKS PARAMETER FROM ANDREY G. KALINICHEV ET AL JPCB 108:1255 (2004)
REMARKS NO PARAMETERS FOR DIHEDRALS AND IMPROPERS
set echo=false end
!! - ALL PARAMETERS FROM ANDREY G.KALINICHEV ET AL JPCB 108:1255 (2004)
bond o* h* 554.1349 1.0000 ! water
bond oh ho 554.1349 1.0000 ! hydroxyl group
bond ohs ho 554.1349 1.0000 ! hydroxyl substitution
bond nh nh 220.8000 1.3940 ! amide group (N-N)
bond nh hn 457.4590 1.0260 ! amide group (N-H)
angle h* o* h* 45.7696 109.47 ! water
angle nh nh hn 41.6000 110.00 ! amide (N-N-H)
angle hn nh hn 38.0000 105.50 ! amide (H-N-H)
{* Non Bonded Parameter section *}
{* ============================ *}
!!
!
! atom eps sigma eps (1:4) sigma(1:4)
! type (kcal/mol) (A)
! --------------------------------------------------------------
NONBonded h* 0.0000 0.0000 0.0000 0.0000
NONBonded ho 0.0000 0.0000 0.0000 0.0000
NONBonded o* 0.1554 3.1655 0.1554 3.1655
NONBonded oh 0.1554 3.1655 0.1554 3.1655
NONBonded ob 0.1554 3.1655 0.1554 3.1655
NONBonded obos 0.1554 3.1655 0.1554 3.1655
set echo=true end
Sincerely
Naresh
> ----------------------------------------
> From: johan strumpfer <johan.ks.uiuc_at_gmail.com>
> Sent: Tue Jun 07 16:44:33 CEST 2011
> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> Subject: Re: namd-l: water equilibration
>
>
> Hi Naresh,
>
> As Bjoern said, your input script looks okay so to better diagnose it
> we need more information. Could you rule out that it is not an error
> with the custom force-field file and also post the contents of the log
> file to give us more information.
>
> Cheers,
> Johan
>
> ----------------------------------------------------------------
> Johan Strumpfer (johanstr_at_ks.uiuc.edu)
> Theoretical and Computational Biophysics Group
> 3115 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801, USA
>
>
>
> On Tue, Jun 7, 2011 at 10:03 AM, Narasimhan LOGANATHAN
> <Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
> > Hi,
> > Yes. The custom force-field file is in X-plor format only and still i have the
> > errors.
> >
> > Sincerely,
> > Naresh
> >> ----------------------------------------
> >> From: johan strumpfer <johanstr_at_ks.uiuc.edu>
> >> Sent: Mon Jun 06 15:59:05 CEST 2011
> >> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> >> Subject: Re: namd-l: water equilibration
> >>
> >>
> >> Hi Naresh,
> >>
> >> You set paraTypeCharmm off, this would mean that your custom
> >> force-field is in Xplor format - is this the case?
> >>
> >> Cheers,
> >> Johan
> >>
> >> ------------------------------------------------------------------------------------------------------
> >> Johan Strumpfer: johanstr_at_ks.uiuc.edu www.ks.uiuc.edu/~johanstr
> >> Theoretical and Computational Biophysics Group
> >> 3115 Beckman Institute
> >> University of Illinois at Urbana-Champaign
> >> 405 N. Mathews
> >> Urbana, IL 61801, USA
> >> ------------------------------------------------------------------------------------------------------
> >>
> >>
> >>
> >> On Mon, Jun 6, 2011 at 9:55 AM, Narasimhan LOGANATHAN
> >> <Narasimhan.Loganathan_at_etu.univ-provence.fr> wrote:
> >> > Hi,
> >> >
> >> > Yes. I copied all the error message. It didnt provide any other information on the line which i went wrong.
> >> >
> >> > Sincerely
> >> > Naresh
> >> >> ----------------------------------------
> >> >> From: Wang Yi <dexterwy_at_gmail.com>
> >> >> Sent: Mon Jun 06 15:42:26 CEST 2011
> >> >> To: Narasimhan LOGANATHAN <Narasimhan.Loganathan_at_etu.univ-provence.fr>
> >> >> Subject: Re: namd-l: water equilibration
> >> >>
> >> >>
> >> >> Hey Naresh,
> >> >>
> >> >> Did you copy-and-paste all the error message? Usually in addition to "FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE". NAMD should also tell you the line at which the execution went into error. Do you have that?
> >> >> ___________________________
> >> >>
> >> >> Yi (Yves) Wang
> >> >> Duke University
> >> >>
> >> >>
> >> >>
> >> >>
> >> >>
> >> >> ? 2011-6-6???9:07? Narasimhan LOGANATHAN ???
> >> >>
> >> >> > Hi all,
> >> >> > I am a newbie to NAMD. Right now i am trying to equilibrate water box.
> >> >> > I am not using the CHARMM forcefield. Hence i defined my own parameter file.
> >> >> > However when i tried to equilibrate or minimize the water i am getting the error
> >> >> >
> >> >> > ------------- Processor 0 Exiting: Called CmiAbort ------------
> >> >> > Reason: FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> >> >> >
> >> >> > Charm++ fatal error:
> >> >> > FATAL ERROR: ERROR(S) IN THE CONFIGURATION FILE
> >> >> >
> >> >> >
> >> >> >
> >> >> > Herewith, i have attached the config file. Could someone let me know how can i proceed.
> >> >> >
> >> >> > structure water.psf
> >> >> > coordinates water.pdb
> >> >> >
> >> >> > set temperature 300 ;# Tcl variable
> >> >> > set outputname water-equi ;# Tcl variable
> >> >> >
> >> >> >
> >> >> > temperature $temperature ;# intialize velocities randomly using Boltzmann Distribution
> >> >> >
> >> >> > firsttimestep 0
> >> >> >
> >> >> > ## Input and ForceField Parameters ##
> >> >> > paratypeCharmm off
> >> >> > parameters clayff-namd.inp
> >> >> >
> >> >> > if {0} {
> >> >> > cellBasisVector1 31.212 0.0 0.0
> >> >> > cellBasisVector2 0.0 27.000 0.0
> >> >> > cellBasisVector3 0.0 0.0 30.000
> >> >> > cellOrigin 0.0 0.0 0.0
> >> >> > }
> >> >> >
> >> >> >
> >> >> > ##exclude scaled1-4 ##
> >> >> > ##1-4scaling 1.0 ##
> >> >> > cutoff 12.0
> >> >> > ##switching off ##
> >> >> > ## swtichdist 10.0 ## to be used when switching is on ##
> >> >> > pairlistdist 14.0 ;# cutoff + 2 in general
> >> >> > wrapAll on
> >> >> >
> >> >> > ## Integrator Parameters ##
> >> >> >
> >> >> > stepspercycle 2 ;# redefine pairlists every this many timesteps
> >> >> > timestep 1.0 ;# 1 fs/step
> >> >> > rigidBonds all ;# to keep the water molecules rigid
> >> >> > nonbondedFreq 1 ;# no. of timesteps used to calculate nonbonded interactions
> >> >> > fullElectFrequency 1 ;# no. of timesteps used to calculate electrostatic interactions
> >> >> >
> >> >> > ## Constant Temperature Control ##
> >> >> > langevin on ;# Uses langevin dynamics for controlling T (or) P
> >> >> > langevinDamping 1.0 ;# Damping Coefficient in pico seconds
> >> >> > langevinTemp $temperature ;# random noise at this level
> >> >> > langevinHydrogen no ;# no coupling of hydrogens
> >> >> >
> >> >> > ## Constant Pressure Control is done by the use of the langevin dynamics (see manual) ##
> >> >> >
> >> >> >
> >> >> > ## Particle Mesh Ewald ##
> >> >> > PME yes
> >> >> > PMEGridSpacing 1.0 ;# Alternatively we can specify the PMEgrid Manually in case direction ##
> >> >> >
> >> >> > #################################################################
> >> >> > ### Output Options ###
> >> >> > #################################################################
> >> >> >
> >> >> > outputname $outputname
> >> >> > restartfreq 500
> >> >> > dcdFreq 500
> >> >> > xstFreq 200
> >> >> > outputEnergies 100
> >> >> > outputPressure 100
> >> >> >
> >> >> >
> >> >> > ###################################################################
> >> >> > ### IMD Settings ###
> >> >> > ###################################################################
> >> >> >
> >> >> > if{0} {
> >> >> > IMDon on
> >> >> > IMDport 3000 ;# Enter this port number in VMD ##
> >> >> > IMDfreq 1 ;# send every 1 frame ##
> >> >> > IMDwait no ;# wait for VMD to connect before running ##
> >> >> > }
> >> >> >
> >> >> >
> >> >> > ###################################################################
> >> >> > ### Execution Script ###
> >> >> > ###################################################################
> >> >> > ## Minimization ##
> >> >> > if {0} {
> >> >> > minimize 100
> >> >> > reinitvels $temperature
> >> >> > }
> >> >> >
> >> >> > run 100000
> >> >> >
> >> >> > Thanks in advance
> >> >> > Naresh
> >> >> >
> >> >> >
> >> >>
> >> >
> >> >
> >>
> >
>
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