VMD-L Mailing List

From: Research Jubilant (research.jubilant_at_gmail.com)
Date: Wed Apr 17 2013 - 16:54:08 CDT

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> 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
> 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
> ==============================**==============================**==========
>
>