Abnormal EOF found -buffer=*END*

From: Patrick Yee (pyee_at_nd.edu)
Date: Mon Nov 02 2009 - 12:35:52 CST

Hi everyone -

I am continually getting the error: FATAL ERROR: ABNORMAL EOF FOUND -
buffer=*END* whenever I try to run: "namd2 argon_NVT.conf"

The full text of my the program is:

Charm++: standalone mode (not using charmrun)
Info: NAMD 2.6 for Linux-amd64
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Based on Charm++/Converse 50900 for net-linux-amd64-iccstatic
Info: Built Wed Aug 30 12:54:51 CDT 2006 by jim on belfast.ks.uiuc.edu
Info: 1 NAMD 2.6 Linux-amd64 1 newcell.crc.nd.edu pyee
Info: Running on 1 processors.
Info: 7476 kB of memory in use.
Info: Memory usage based on mallinfo
Info: Configuration file is argon_NVT.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 10
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 10
Info: PERIODIC CELL BASIS 1 10.229 0 0
Info: PERIODIC CELL BASIS 2 0 10.229 0
Info: PERIODIC CELL BASIS 3 0 0 10.229
Info: PERIODIC CELL CENTER 5.1145 5.1145 5.1145
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 2000 steps
Info: FIRST LDB TIMESTEP 50
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: MIN ATOMS PER PATCH 100
Info: INITIAL TEMPERATURE 94.4
Info: CENTER OF MASS MOVING INITIALLY? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: DCD FILENAME argon_NVT.dcd
Info: DCD FREQUENCY 25
Info: DCD FIRST STEP 25
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME argon_NVT.xst
Info: XST FREQUENCY 25
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME argon_NVT
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME argon_NVT.restart
Info: RESTART FREQUENCY 50
Info: BINARY RESTART FILES WILL BE USED
Info: SWITCHING ACTIVE
Info: SWITCHING ON 6
Info: SWITCHING OFF 7.65
Info: PAIRLIST DISTANCE 9.35
Info: PAIRLIST SHRINK RATE 0.01
Info: PAIRLIST GROW RATE 0.01
Info: PAIRLIST TRIGGER 0.3
Info: PAIRLISTS PER CYCLE 2
Info: PAIRLISTS ENABLED
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 11.85
Info: ENERGY OUTPUT STEPS 10
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 100
Info: PRESSURE OUTPUT STEPS 10
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 94.4
Info: LANGEVIN DAMPING COEFFICIENT IS 5 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 1257186464
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB ../RahmanSimulation/argon.pdb
Info: STRUCTURE FILE ../RahmanSimulation/argon.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS ../RahmanSimulation/argonFF.inp
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Info: SUMMARY OF PARAMETERS:
Info: 0 BONDS
Info: 0 ANGLES
Info: 0 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 1 VDW
Info: 0 VDW_PAIRS
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*

------------- Processor 0 Exiting: Called CmiAbort ------------
Reason: FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*

Stack Traceback:
  [0] CmiAbort+0x4f [0x7eb405]
  [1] _Z8NAMD_diePKc+0x62 [0x4b31e2]
  [2] _Z14NAMD_read_lineP8_IO_FILEPc+0xf1 [0x4b6d25]
  [3] _ZN8Molecule13read_psf_fileEPcP10Parameters+0xad2 [0x692d06]
  [4] _ZN8MoleculeC9EP13SimParametersP10ParametersPc+0x24f [0x692145]
  [5] _ZN8MoleculeC1EP13SimParametersP10ParametersPc+0x6 [0x696e64]
  [6] _ZN9NamdState14configListInitEP10ConfigList+0x642 [0x6ae84c]
  [7] _ZN9ScriptTcl9initcheckEv+0x5e [0x6ff8ac]
  [8] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e [0x6fc472]
  [9] TclInvokeStringCommand+0x91 [0x80cc78]
  [10] namd2 [0x842ac8]
  [11] Tcl_EvalEx+0x176 [0x84310b]
  [12] Tcl_EvalFile+0x134 [0x83ab14]
  [13] _ZN9ScriptTcl3runEPc+0x14 [0x6fb99e]
  [14] main+0x21b [0x4b69c3]
  [15] __libc_start_main+0xf4 [0x3a5161d994]
  [16] _ZNSt8ios_base4InitD1Ev+0x3a [0x4b2b5a]
Charm++ fatal error:
FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*

Abort

I tried looking over the archives, but this did not work. My system is a
simple argon one having a very simple parameter file with the text:

  BONDS

ANGLES

DIHEDRALS

IMPROPERS

!
!CMAP
!

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
                !adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!carbons
Ar 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO

HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
                 ! READ PARAM APPEND CARD
                 ! to append hbond parameters from the file: par_hbond.inp

END
BONDS

ANGLES

DIHEDRALS

IMPROPERS

!
!CMAP
!

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
                !adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!carbons
Ar 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO

HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use
                 ! READ PARAM APPEND CARD
                 ! to append hbond parameters from the file: par_hbond.inp

END

I tried messing around with the spacing, as other people with this error
have, but I haven't had any luck. Does anyone have any suggestions?

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