VMD-L Mailing List

From: Research Jubilant (research.jubilant_at_gmail.com)
Date: Wed Apr 17 2013 - 18:48:41 CDT

I don't have any carbohydrate part in my system. If I comment out that the
following in my conf file, it works just fine.

!SOD OC2D2 -0.075020 3.190 ! For carb carboxylate groups
!SOD OG2D2 -0.075020 3.190 ! For CGenFF carboxylate groups

Thanks

On Wed, Apr 17, 2013 at 5:57 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:

> 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>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
>> ======================================================================
>>
>>
>
>