From: Aron Broom (broomsday_at_gmail.com)
Date: Mon Mar 05 2012 - 08:31:31 CST
I'm not certain, but it sounds like one of your input files has been
damaged. Maybe download them again, or test using a different version than
27?
On Mon, Mar 5, 2012 at 9:12 AM, raghav singh <raghavbioinfo_at_gmail.com>wrote:
> Hello All,
>
> I am trying to run SMD simulation on ssDNA... but getting this ( ABNORMAL
> EOF FOUND - buffer=*END*) error. I have already looked through archives and
> there is no satisfactory suggestion is posted.
> if the guys who already gone through these problems have any suggestion or
> solution ... Please suggest me.
>
> Thank You
>
> Raghav
>
> Info: SIMULATION PARAMETERS:
> Info: TIMESTEP 2
> Info: NUMBER OF STEPS 0
> Info: STEPS PER CYCLE 10
> Info: LOAD BALANCER Centralized
> Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
> Info: LDB PERIOD 2000 steps
> Info: FIRST LDB TIMESTEP 50
> Info: LAST LDB TIMESTEP -1
> Info: LDB BACKGROUND SCALING 1
> Info: HOM BACKGROUND SCALING 1
> Info: MIN ATOMS PER PATCH 40
> Info: INITIAL TEMPERATURE 300
> Info: CENTER OF MASS MOVING INITIALLY? NO
> Info: DIELECTRIC 1
> Info: EXCLUDE SCALED ONE-FOUR
> Info: 1-4 ELECTROSTATICS SCALED BY 1
> Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
> Info: DCD FILENAME single_ww_pcv.dcd
> Info: DCD FREQUENCY 500
> Info: DCD FIRST STEP 500
> Info: XST FILENAME single_ww_pcv.xst
> Info: XST FREQUENCY 500
> Info: NO VELOCITY DCD OUTPUT
> Info: NO FORCE DCD OUTPUT
> Info: OUTPUT FILENAME single_ww_pcv
> Info: BINARY OUTPUT FILES WILL BE USED
> Info: RESTART FILENAME single_ww_pcv.restart
> Info: RESTART FREQUENCY 500
> Info: BINARY RESTART FILES WILL BE USED
> Info: SWITCHING ACTIVE
> Info: SWITCHING ON 10
> Info: SWITCHING OFF 12
> Info: PAIRLIST DISTANCE 13.5
> 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 0.48
> Info: HYDROGEN GROUP CUTOFF 2.5
> Info: PATCH DIMENSION 16.48
> Info: ENERGY OUTPUT STEPS 100
> Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> Info: TIMING OUTPUT STEPS 1000
> Info: PRESSURE OUTPUT STEPS 100
> Info: FIXED ATOMS ACTIVE
> Info: SMD ACTIVE
> Info: SMD VELOCITY 0.005 ANGSTROM/TIMESTEP
> Info: SMD DIRECTION -0.0259491 0.998205 0.0539723
> Info: SMD K 7
> Info: SMD K2 0
> Info: SMD OUTPUT FREQUENCY 10 TIMESTEPS
> Info: SMD FILE smd1_ww_eq.ref
> Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
> Info: TARGET PRESSURE IS 1.01325 BAR
> Info: OSCILLATION PERIOD IS 100 FS
> Info: DECAY TIME IS 50 FS
> Info: PISTON TEMPERATURE IS 300 K
> Info: PRESSURE CONTROL IS GROUP-BASED
> Info: INITIAL STRAIN RATE IS 0 0 0
> Info: CELL FLUCTUATION IS ISOTROPIC
> Info: USING VERLET I (r-RESPA) MTS SCHEME.
> Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
> Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
> Info: RIGID BONDS TO HYDROGEN : ALL
> Info: ERROR TOLERANCE : 1e-08
> Info: MAX ITERATIONS : 100
> Info: RIGID WATER USING SETTLE ALGORITHM
> Info: RANDOM NUMBER SEED 1330956154
> Info: USE HYDROGEN BONDS? NO
> Info: COORDINATE PDB smd1_ww_eq.pdb
> Info: STRUCTURE FILE smd1_autopsf.psf
> Info: PARAMETER file: CHARMM format!
> Info: PARAMETERS par_all27_prot_na.inp
> Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> FATAL ERROR: ABNORMAL EOF FOUND - buffer=*END*
>
>
-- Aron Broom M.Sc PhD Student Department of Chemistry University of Waterloo
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