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
__________________________________________________
Do You Yahoo!?
Tired of spam? Yahoo! Mail has the best spam protection around
http://mail.yahoo.com
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:41:26 CST