VMD-L Mailing List
From: Research Jubilant (research.jubilant_at_gmail.com)
Date: Wed Apr 17 2013 - 12:51:08 CDT
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- Reply: Mayne, Christopher G: "Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC*"
- Reply: Jeffrey Potoff: "Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC*"
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Hello All,
I have the following error during my NAMD run. Can anyone help me solve
this?
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
/home/sundar/NAMD_conf_FF_TCL/FF/toppar/toppar_water_ions.str
LINE=*set nat ?NATC*
Charm++ fatal error:
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE
/home/sundar/NAMD_conf_FF_TCL/FF/toppar/toppar_water_ions.str
LINE=*set nat ?NATC*
Abort
The following is my conf file.
#Set file names:
set name prot_popcwi
set parfile1 /toppar/par_all36_prot.prm ;# CHARMM 36 parameterfile
for protein
set parfile2 /toppar/par_all36_lipid.prm ;# CHARMM 36 parameterfile
for lipids
set parfile3 /toppar/toppar_water_ions.str ;# CHARMM 36
parameterfile for water and ions
set output prot_minieqtail
set const notail.cnst #only lipid tails are
free
###############################################################################
# Read in system:
structure ${name}.psf
coordinates ${name}.pdb
outputname $output
# Set system size and origin for PBC:
set cbv1 124 ;# Box size in X dimension
set cbv2 124 ;# Box size in Y dimension
set cbv3 160 ;# Box size in Z dimension
set cox 0.046737585216760635 ;# X coordinate for cell origin
set coy 0.42250680923461914 ;# Y coordinate for cell origin
set coz -21.4572811126709 ;# Z coordinate for cell origin
# Set grid size for pmE:
set PMEGS 1.0 ;# The grid spacing must be at
least PMEGridSpacing
#Set variables for simulation
set T 310.
set sdist 10. ;# Distance for switching function
set cdist 12. ;# Distance for nonbond cutoff (sdist + 2)
set pdist 13.5 ;# PairListDist, atom move <2A pr. cycle
set sprc 10 ;# How often is the Pairlist redone??? use 10 for
2fs timestep
set timing 50 ;# How often to write timing information
set minstep 20000 ;# Number of steps for minimizations
firsttimestep 0
set eqstep 250000
set tstep 2.0 ;# Run simulation with 1 fs timestep
set nbf 1 ;# How often to calculate nonbonded???
set fef 2 ;# How often to do full electrostatics???
set outputfreq 500 ;# How often is output written to log file?
set dcdfreq 500 ;# How often is snapshot written to dcd
file?
set restfreq 500 ;# How often are the restart files written?
###########################################################################
# Force field parameters #
###########################################################################
#Specify force field
paraTypeCharmm on
parameters $parfile1
parameters $parfile2
parameters $parfile3
exclude scaled1-4
1-4scaling 1.0
switching on
cutoff $cdist
switchdist $sdist
pairlistdist $pdist
###########################################################################
# Temperature #
###########################################################################
#Minimization so temperature is set to 0 K
temperature $T
###############################################################################
# Periodic Boundary System
###############################################################################
# Only to be given in first step of simulation
cellBasisVector1 $cbv1 0. 0.
cellBasisVector2 0. $cbv2 0.
cellBasisVector3 0. 0. $cbv3
cellOrigin $cox $coy $coz
#Wrap periodic cells
wrapWater on
wrapAll on
###############################################################################
# # Integrator Parameters
###############################################################################
timestep 2.0 ;# 2fs/step
rigidBonds all ;# needed for 2fs steps
nonbondedFreq $nbf
fullElectFrequency $fef
stepspercycle $sprc
###############################################################################
# Electrostatics
###############################################################################
# Use Particle Mesh Ewald:
PME yes
PMEGridSpacing $PMEGS
###############################################################################
# Constant Temperature Control
###############################################################################
# Constant Temperature Control
langevin on ;# do langevin dynamics
langevinDamping 1 ;# damping coefficient (gamma) of 5/ps
langevinTemp $T
###########################################################################
# Constraint parameters #
###########################################################################
# Fixed Atoms Constraint (set PDB beta-column to 1)
fixedAtoms on
fixedAtomsFile $const
fixedAtomsCol B
fixedAtomsForces on
###########################################################################
# Energies & Miscellaneous #
###########################################################################
# Write energies to log-file:
outputEnergies $outputfreq
outputPressure $outputfreq
outputTiming $dcdfreq
binaryoutput no
DCDfile $output.dcd
DCDfreq $dcdfreq
DCDUnitCell yes
binaryrestart yes
restartname $output.restart
restartfreq $restfreq
XSTfile $output.xst
XSTfreq $dcdfreq
###########################################################################
# Minimization and Equilibration #
###########################################################################
if {1} {
minimize $minstep ;# Minimize system with 'numsteps' steps.
reinitvels $T ;# reinitiate velocities to the desired
temperature
}
run $eqstep ;# 0.5 ns equilibrations
-Thanks
J
- Next message: Salomon Turgman Cohen: "Re: command line rep creation"
- Previous message: Mayne, Christopher G: "Re: Is it necessary to set up more than 1 hydrogen bonding for one Acceptor in Water Int. in ffTK"
- Next in thread: Mayne, Christopher G: "Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC*"
- Reply: Mayne, Christopher G: "Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC*"
- Reply: Jeffrey Potoff: "Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE toppar_water_ions.str LINE=*set nat ?NATC*"
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