Tutorial-l Mailing List

From: RICARDO VAZQUEZ (ricardo1v_at_yahoo.com)
Date: Fri May 20 2011 - 22:09:08 CDT

Hi,
I tryed to run the tutorial for ubq. But don't run, I used the files.ubq_wb_eq.confubq_wb.pdbubq_wb.psf
I not sure maybe I need restart the installation.Thank you in advance for your help.Ricardo Vazquez
The message is:
mac-pro:TUTORIAL eon$  /Users/eon/NAMD27/namd2     /Users/eon/NAMD27/MOLECULAS/TUTORIAL/ubq_wb_eq.conf      /Users/eon/NAMD27/TOPPAR/par_all27_prot_lipid.inp +p8Charm++: standalone mode (not using charmrun)Charm++: scheduler running in netpoll mode.Charm++> Running on 1 unique compute nodes.Charm++> Cpu topology info:PE to node map: 0 0 0 0 0 0 0 0 Node to PE map:Chip #0: 0 1 2 3 4 5 6 7 Charm++> cpu topology info is gathered in 0.001 seconds.Info: NAMD 2.7 for MacOSX-x86Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/Info: and send feedback or bug reports to namd_at_ks.uiuc.eduInfo: Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)Info: in all publications reporting results obtained with NAMD.Info: Info: Based on Charm++/Converse 60202 for multicore-darwin-x86Info: Built Wed Oct 13 11:34:26 CDT 2010 by jim on juneau.ks.uiuc.eduInfo: 1 NAMD  2.7  MacOSX-x86  8    my-selfs-mac-pro.local  eonInfo: Running on
 8 processors.Info: CPU topology information available.Info: Charm++/Converse parallel runtime startup completed at 0.0163469 sInfo: 605.176 MB of memory in use based on psInfo: Found 2 config files.Info: Changed directory to /Users/eon/NAMD27/MOLECULAS/TUTORIALInfo: Configuration file is ubq_wb_eq.confTCL: Suspending until startup complete.Info: SIMULATION PARAMETERS:Info: TIMESTEP               2Info: NUMBER OF STEPS        0Info: STEPS PER CYCLE        10Info: PERIODIC CELL BASIS 1  42 0 0Info: PERIODIC CELL BASIS 2  0 44 0Info: PERIODIC CELL BASIS 3  0 0 47Info: PERIODIC CELL CENTER   31 29 17.5Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.Info: LOAD BALANCER  CentralizedInfo: LOAD BALANCING STRATEGY  New Load Balancers -- ASBInfo: LDB PERIOD             2000 stepsInfo: FIRST LDB TIMESTEP     50Info: LAST LDB TIMESTEP     -1Info: LDB BACKGROUND SCALING 1Info: HOM BACKGROUND SCALING 1Info: PME
 BACKGROUND SCALING 1Info: MAX SELF PARTITIONS    20Info: MAX PAIR PARTITIONS    8Info: SELF PARTITION ATOMS   154Info: SELF2 PARTITION ATOMS   154Info: PAIR PARTITION ATOMS   318Info: PAIR2 PARTITION ATOMS  637Info: MIN ATOMS PER PATCH    100Info: INITIAL TEMPERATURE    310Info: CENTER OF MASS MOVING INITIALLY? NOInfo: DIELECTRIC             1Info: EXCLUDE                SCALED ONE-FOURInfo: 1-4 ELECTROSTATICS SCALED BY 1Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USEDInfo: DCD FILENAME           ubq_wb_eq.dcdInfo: DCD FREQUENCY          250Info: DCD FIRST STEP         250Info: DCD FILE WILL CONTAIN UNIT CELL DATAInfo: XST FILENAME           ubq_wb_eq.xstInfo: XST FREQUENCY          250Info: NO VELOCITY DCD OUTPUTInfo: OUTPUT FILENAME        ubq_wb_eqInfo: BINARY OUTPUT FILES WILL BE USEDInfo: RESTART FILENAME       ubq_wb_eq.restartInfo: RESTART FREQUENCY      500Info: BINARY RESTART FILES WILL
 BE USEDInfo: SWITCHING ACTIVEInfo: SWITCHING ON           10Info: SWITCHING OFF          12Info: PAIRLIST DISTANCE      14Info: PAIRLIST SHRINK RATE   0.01Info: PAIRLIST GROW RATE     0.01Info: PAIRLIST TRIGGER       0.3Info: PAIRLISTS PER CYCLE    2Info: PAIRLISTS ENABLEDInfo: MARGIN                 0.495Info: HYDROGEN GROUP CUTOFF  2.5Info: PATCH DIMENSION        16.995Info: ENERGY OUTPUT STEPS    100Info: CROSSTERM ENERGY INCLUDED IN DIHEDRALInfo: TIMING OUTPUT STEPS    1000Info: PRESSURE OUTPUT STEPS  100Info: LANGEVIN DYNAMICS ACTIVEInfo: LANGEVIN TEMPERATURE   310Info: LANGEVIN DAMPING COEFFICIENT IS 1 INVERSE PSInfo: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENSInfo: LANGEVIN PISTON PRESSURE CONTROL ACTIVEInfo:        TARGET PRESSURE IS 1.01325 BARInfo:     OSCILLATION PERIOD IS 100 FSInfo:             DECAY TIME IS 50 FSInfo:     PISTON TEMPERATURE IS 310 KInfo:       PRESSURE CONTROL IS
 GROUP-BASEDInfo:    INITIAL STRAIN RATE IS 0 0 0Info:       CELL FLUCTUATION IS ISOTROPICInfo: PARTICLE MESH EWALD (PME) ACTIVEInfo: PME TOLERANCE               1e-06Info: PME EWALD COEFFICIENT       0.257952Info: PME INTERPOLATION ORDER     4Info: PME GRID DIMENSIONS         44 44 48Info: PME MAXIMUM GRID SPACING    1Info: Attempting to read FFTW data from FFTW_NAMD_2.7_MacOSX-x86.txtInfo: Optimizing 6 FFT steps.  1... 2... 3... 4... 5... 6...   Done.Info: Writing FFTW data to FFTW_NAMD_2.7_MacOSX-x86.txtInfo: FULL ELECTROSTATIC EVALUATION FREQUENCY      2Info: USING VERLET I (r-RESPA) MTS SCHEME.Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICSInfo: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPSInfo: RIGID BONDS TO HYDROGEN : ALLInfo:         ERROR TOLERANCE : 1e-08Info:          MAX ITERATIONS : 100Info: RIGID WATER USING SETTLE ALGORITHMInfo: RANDOM NUMBER SEED     1305945994Info: USE HYDROGEN BONDS?    NOInfo:
 COORDINATE PDB         /Users/eon/NAMD27/MOLECULAS/TUTORIAL/ubq_wb.pdbInfo: STRUCTURE FILE         /Users/eon/NAMD27/MOLECULAS/TUTORIAL/ubq_wb.psfInfo: PARAMETER file: CHARMM format! Info: PARAMETERS             /Users/eon/NAMD27/TOPPAR/par_all27_prot_lipid.inpInfo: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERSInfo: SUMMARY OF PARAMETERS:Info: 179 BONDSInfo: 441 ANGLESInfo: 534 DIHEDRALInfo: 49 IMPROPERInfo: 0 CROSSTERMInfo: 89 VDWInfo: 0 VDW_PAIRSFATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR C  NH1  CT1  C  NH1  CT1  C  NH1------------- Processor 0 Exiting: Called CmiAbort ------------Reason: FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR C  NH1  CT1  C  NH1  CT1  C  NH1
Charm++ fatal error:FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR C  NH1  CT1  C  NH1  CT1  C  NH1
Abort trapmac-pro:TUTORIAL eon$  

**
** Visit http://www.greatcircle.com/majordomo/ for more info on majordomo
**