From: Mayne, Christopher G (cmayne2_at_illinois.edu)
Date: Wed Apr 17 2013 - 22:18:05 CDT

If I recall correctly in CHARMM36 the sodium ion parameters were updated, including an NBFIX term to correct for the over estimation for the interaction of sodium ions with highly charged oxygen atoms--which is what this entry is.

The error indicates that the NONBONDED entry for OC2D2 hasn't been read in. It is either required because it is located in your system, or as is likely the case here, because it's related to another parameter (i.e., NBFIX). If you don't have and OC2D2 or OG2D2 atom type in your system, just comment out these NBFIX terms and be done with it.

I might also add that it's worth reading the errors NAMD is generating carefully--it's telling you exactly what's wrong. Secondly, taking some time to understand parameter files will make solving these issues (and many others) trivial.

Christopher Mayne

On Apr 17, 2013, at 6:48 PM, Research Jubilant wrote:

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<mailto: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<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

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Associate Professor and Director of Early Engineering Programs
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http://potoff1.eng.wayne.edu>
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