FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7

From: Shirley Li (li19104_at_yahoo.com)
Date: Wed Dec 21 2005 - 14:56:36 CST

Dear NAMD experts,
 
 I was trying to minimize a protein-water-ion system, but the minimization crashed with the error message "FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7". There isn't any CN7 atom in my system. Does anybody know what's wrong?
 
 BTW, my protein contains several chains, and each chain was constructed separately, which was then merged together to form the entire protein. So there are certainly close contacts in the system. I wonder if clashes could cause the above "FATAL ERROR"?
 
 Any help will be greatly appreciated.
 
 Shirley
 
 
 The full output for the minimization is as follows:
 
 =============================
 Charm++: scheduler running in netpoll mode.
 Info: NAMD 2.6b1 for Linux-i686-TCP
 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 Kale et al., J. Comp. Phys. 151:283-312 (1999)
 Info: in all publications reporting results obtained with NAMD.
 Info:
 Info: Based on Charm++/Converse 50900 for net-linux-tcp-iccstatic
 Info: Built Fri Jul 29 11:31:45 CDT 2005 by jim on verdun.ks.uiuc.edu
 Info: Sending usage information to NAMD developers via UDP. Sent data is:
 Info: 1 NAMD 2.6b1 Linux-i686-TCP 16 compute-1-16.local xiange
 Info: Running on 16 processors.
 Info: 7991 kB of memory in use.
 Info: Configuration file is min.conf
 TCL: Suspending until startup complete.
 Info: SIMULATION PARAMETERS:
 Info: TIMESTEP 1
 Info: NUMBER OF STEPS 0
 Info: STEPS PER CYCLE 20
 Info: PERIODIC CELL BASIS 1 149.057 0 0
 Info: PERIODIC CELL BASIS 2 0 112.312 0
 Info: PERIODIC CELL BASIS 3 0 0 144.688
 Info: PERIODIC CELL CENTER -5.763 12.999 50.491
 Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
 Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
 Info: LOAD BALANCE STRATEGY Other
 Info: LDB PERIOD 4000 steps
 Info: FIRST LDB TIMESTEP 100
 Info: LDB BACKGROUND SCALING 1
 Info: HOM BACKGROUND SCALING 1
 Info: PME 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 0
 Info: CENTER OF MASS MOVING? NO
 Info: DIELECTRIC 1
 Info: EXCLUDE SCALED ONE-FOUR
 Info: 1-4 SCALE FACTOR 1
 Info: NO DCD TRAJECTORY OUTPUT
 Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
 Info: NO VELOCITY DCD OUTPUT
 Info: OUTPUT FILENAME min-all_end
 Info: RESTART FILENAME min-all_rest
 Info: RESTART FREQUENCY 2000
 Info: SWITCHING ACTIVE
 Info: SWITCHING ON 8.5
 Info: SWITCHING OFF 10
 Info: PAIRLIST DISTANCE 11.5
 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 5
 Info: HYDROGEN GROUP CUTOFF 2.5
 Info: PATCH DIMENSION 19
 Info: ENERGY OUTPUT STEPS 2000
 Info: TIMING OUTPUT STEPS 2000
 Info: FIXED ATOMS ACTIVE
 Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
 Info: LANGEVIN DYNAMICS ACTIVE
 Info: LANGEVIN TEMPERATURE 75
 Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS
 Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
 Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
 Info: TARGET PRESSURE IS 1.01325 BAR
 Info: OSCILLATION PERIOD IS 200 FS
 Info: DECAY TIME IS 100 FS
 Info: PISTON TEMPERATURE IS 75 K
 Info: PRESSURE CONTROL IS GROUP-BASED
 Info: INITIAL STRAIN RATE IS 0 0 0
 Info: CELL FLUCTUATION IS ANISOTROPIC
 Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE
 Info: PARTICLE MESH EWALD (PME) ACTIVE
 Info: PME TOLERANCE 1e-06
 Info: PME EWALD COEFFICIENT 0.312341
 Info: PME INTERPOLATION ORDER 4
 Info: PME GRID DIMENSIONS 150 120 150
 Info: Attempting to read FFTW data from FFTW_NAMD_2.6b1_Linux-i686-TCP.txt
 Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
 Info: Writing FFTW data to FFTW_NAMD_2.6b1_Linux-i686-TCP.txt
 Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
 Info: USING VERLET I (r-RESPA) MTS SCHEME.
 Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
 Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
 Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
 Info: RANDOM NUMBER SEED 1135197169
 Info: USE HYDROGEN BONDS? NO
 Info: COORDINATE PDB result_wbi.pdb
 Info: STRUCTURE FILE result_wbi.psf
 Info: PARAMETER file: CHARMM format!
 Info: PARAMETERS par_all27_prot_na.inp
 Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
 Info: SUMMARY OF PARAMETERS:
 Info: 250 BONDS
 Info: 622 ANGLES
 Info: 1049 DIHEDRAL
 Info: 73 IMPROPER
 Info: 130 VDW
 Info: 0 VDW_PAIRS
 Warning: Ignored 181 bonds with zero force constants.
 Warning: Will get H-H distance in rigid H2O from H-O-H angle.
 FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR CN7 CN7 CN7
 
 
 
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