VMD-L Mailing List

From: Research Jubilant (research.jubilant_at_gmail.com)
Date: Thu Apr 18 2013 - 13:03:53 CDT

Thank you very much for your explanation. I'll spend time understanding the
parameter files.

On Wed, Apr 17, 2013 at 10:18 PM, Mayne, Christopher G <cmayne2_at_illinois.edu
> wrote:

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