charmm toppar in namd

From: Matthew B. Roark (Roarkma_at_wabash.edu)
Date: Thu May 31 2012 - 14:04:18 CDT

I am having problems using CHARMM toppar files in NAMD. This is my first time trying to use them in this manner. I'll give what seems to be the most relevant information.
My config file reads:
=============================================================
cellBasisVector1 83.1226654 0.0 0.0
cellBasisVector2 0.0 97.9278107 0.0
cellBasisVector3 0.0 0.0 95.8185654
cellOrigin 0.0 0.0 0.0

coordinates namd.pdb
temperature 318
seed 54229

binaryrestart on
switching on
switchdist 10
cutoff 12
pairlistdist 14
margin 2
stepspercycle 20
paraTypeXplor off
paraTypeCharmm on

PME yes
PMEGridSpacing 1.0
#PMEGridSizeX 96
#PMEGridSizeY 96
#PMEGridSizeZ 108

structure namd.xplor.psf
parameters par_all22_prot.inp
parameters par_all36_lipid_1a.str

parameters top_all22_prot.inp
parameters top_all36_lipid_1a.str
parameters toppar_all36_feller.str
parameters toppar_all36_lipid_cholesterol.str
parameters toppar_all22_prot_retinol.str
parameters toppar_cyp_lyr.str
exclude scaled1-4
1-4scaling 1.0

useGroupPressure yes
useFlexibleCell yes
useConstantArea no
rigidBonds all

langevinPiston on
langevinPistonTarget 1.01325 ;# pressure in bar -> 1 atm
langevinPistonPeriod 200. ;# oscillation period around 100 fs
langevinPistonDecay 100. ;# oscillation decay time of 50 fs
langevinPistonTemp 318 ;# coupled to heat bath

langevin on
langevinTemp 318
langevinDamping 5
langevinHydrogen off

timestep 2.0
fullElectFrequency 4

numsteps 1000
outputtiming 500
restartfreq 500
dcdfreq 500
xstFreq 500
outputEnergies 500
outputname pdpc_rhod
=============================================================

and the ending portion of my NAMD output reads:
=============================================================
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all22_prot.inp
Info: PARAMETERS par_all36_lipid_1a.str
Info: PARAMETERS top_all22_prot.inp
Info: PARAMETERS top_all36_lipid_1a.str
Info: PARAMETERS toppar_all36_feller.str
Info: PARAMETERS toppar_all36_lipid_cholesterol.str
Info: PARAMETERS toppar_all22_prot_retinol.str
Info: PARAMETERS toppar_cyp_lyr.str
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE top_all22_prot.inp
LINE=*31 1*
------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE top_all22_prot.inp
LINE=*31 1*

[0] Stack Traceback:
  [0:0] CmiAbort+0x76 [0xac10e3]
  [0:1] _Z8NAMD_diePKc+0x4a [0x53372a]
  [0:2] _ZN10Parameters26read_charmm_parameter_fileEPc+0x453 [0x960c03]
  [0:3] _ZN10ParametersC1EP13SimParametersP10StringList+0x22f [0x96bb8f]
  [0:4] _ZN9NamdState14configListInitEP10ConfigList+0x1e24 [0x94bb94]
  [0:5] _ZN9ScriptTcl9initcheckEv+0x69 [0x9ad5a9]
  [0:6] _ZN9ScriptTcl3runEv+0xa5 [0x9b0c65]
  [0:7] _Z18after_backend_initiPPc+0x234 [0x536194]
  [0:8] main+0x24 [0x536444]
  [0:9] __libc_start_main+0xf4 [0x325e01d8b4]
  [0:10] cos+0x171 [0x5022b9]
Fatal error on PE 0> FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE top_all22_prot.inp
LINE=*31 1*
=============================================================

I have reviewed the tutorial on CHARMM topology files and this line "31 1" is in the example file. I don't see the problem.

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