From: Joshua D. Moore (jdmoore_at_unity.ncsu.edu)
Date: Wed Dec 21 2005 - 16:57:37 CST
Hi Shirley,
If you get this error, I think you must have CN7 atoms somewhere in your
.psf file. Perhaps you meant to have them as something else? Maybe this
occured as part of your merging?
Josh
On Wed, December 21, 2005 3:56 pm, Shirley Li wrote:
> 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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