From: Chris Harrison (charris5_at_gmail.com)
Date: Mon Mar 05 2012 - 09:11:54 CST
Raghav,
Specifically, the file damaged has an EOF (end-of-file) termination in the
middle of a line somewhere. So look at the end of your psf, pdb and
parameter files in a text editor. Whichever has an abrupt ending in the
middle of it's last line is the culprit file and will need to be recreated.
Best,
Chris
On Mon, Mar 5, 2012 at 8:12 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*
>
>
-- Chris Harrison, Ph.D. NIH Center for Macromolecular Modeling and Bioinformatics Theoretical and Computational Biophysics Group Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801 http://www.ks.uiuc.edu/Research/namd Voice: 773-570-6078 http://www.ks.uiuc.edu/~char Fax: 217-244-6078
This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:17 CST