VMD-L Mailing List

From: Jeffrey Potoff (jpotoffx_at_gmail.com)
Date: Wed Apr 17 2013 - 15:16:06 CDT

Sure. Your parameter file has "charmm speak" in it. These are commands
that are read by the CHARMM simulation engine, but not by NAMD. Remove
these "set nat ..." lines and you should be all set.

Jeff

On 4/17/2013 1:51 PM, Research Jubilant wrote:
> 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
> 

-- 
======================================================================
Jeffrey J. Potoff                         jpotoff_at_wayne.edu
Associate Professor and Director of Early Engineering Programs
Department of Chemical Engineering and Materials Science
Wayne State University			  5050 Anthony Wayne Dr
Detroit, MI 48202
http://potoff1.eng.wayne.edu
======================================================================