VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Wed Apr 17 2013 - 17:57:01 CDT

Did you happen to forget to also load the carbohydrate parameters in
your config file? (par_all36_carb.prm). OC2D2 isn't in toppar_water, and
may just be the first thing NAMD decided to complain about.
-Josh

On 04/17/2013 04:54 PM, Research Jubilant wrote:
> Thanks for that help. I have removed all lines that seemed charmm
> specific to me.
> Now the error is different, FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR
> ATOM TYPE OC2D2
>
> I checked the file for this and its there.
>
> Thanks
>
> J
>
>
> On Wed, Apr 17, 2013 at 3:16 PM, Jeffrey Potoff <jpotoffx_at_gmail.com
> <mailto:jpotoffx_at_gmail.com>> wrote:
>
> 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 <mailto: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
> ======================================================================
>
>