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我用Z-dock对分子进行对接，限定了其中一个蛋白的对接位点，得到的PDB用NAMD进行模拟，运行总是报错。
单独使用这两个蛋白进行模拟，都能正常运行，咨询了一些人，猜测可能是对接这一步产生的PDB文件存在问题需要处理，或者是与力场冲突。
下面是我的run.log， 劳驾各位老师能帮忙看看，实验需要，之前没有接触过这方面，实在没有什么头绪。
Running command: namd2 +p 32 run.conf
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 32 threads
Charm++> Using recursive bisection (scheme 3) for topology aware partitions
Converse/Charm++ Commit ID: v6.7.1-0-gbdf6a1b-namd-charm-6.7.1-build-2016-Nov-07-136676
Warning> Randomization of stack pointer is turned on in kernel, thread migration may not work! Run 'echo 0 > /proc/sys/kernel/randomize_va_space' as root to disable it, or try run with '+isomalloc_sync'.
CharmLB> Load balancer assumes all CPUs are same.
Charm++> Running on 1 unique compute nodes (64-way SMP).
Charm++> cpu topology info is gathered in 0.006 seconds.
Info: NAMD 2.12 for Linux-x86_64-multicore
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: for updates, documentation, and support information.
Info:
Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
Info: in all publications reporting results obtained with NAMD.
Info: Running on 32 processors, 1 nodes, 1 physical nodes.
Info: CPU topology information available.
Info: Charm++/Converse parallel runtime startup completed at 0.0555959 s
CkLoopLib is used in SMP with a simple dynamic scheduling (converse-level notification) but not using node-level queue
Info: 2334.93 MB of memory in use based on /proc/self/stat
Info: Configuration file is run.conf
TCL: Suspending until startup complete.
Warning: The following variables were set in the
Warning: configuration file but will be ignored:
Warning: switchdist (switching)
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 2
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 110 0 0
Info: PERIODIC CELL BASIS 2 0 107.7 0
Info: PERIODIC CELL BASIS 3 0 0 91
Info: PERIODIC CELL CENTER 55.74 54.54 46.12
Info: WRAPPING WATERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: LOAD BALANCER Centralized
Info: LOAD BALANCING STRATEGY New Load Balancers -- DEFAULT
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LAST LDB TIMESTEP -1
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME 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 0.833333
Info: MODIFIED 1-4 VDW PARAMETERS WILL BE USED
Info: DCD FILENAME ./outputs/t1y2020.dcd
Info: DCD FREQUENCY 1000
Info: DCD FIRST STEP 1000
Info: DCD FILE WILL CONTAIN UNIT CELL DATA
Info: XST FILENAME ./outputs/t1y2020.xst
Info: XST FREQUENCY 1000
Info: NO VELOCITY DCD OUTPUT
Info: NO FORCE DCD OUTPUT
Info: OUTPUT FILENAME ./outputs/t1y2020
Info: BINARY OUTPUT FILES WILL BE USED
Info: RESTART FILENAME ./outputs/t1y2020.restart
Info: RESTART FREQUENCY 1000
Info: BINARY RESTART FILES WILL BE USED
Info: CUTOFF 10
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 2
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 18
Info: ENERGY OUTPUT STEPS 100
Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
Info: TIMING OUTPUT STEPS 1000
Info: PRESSURE OUTPUT STEPS 100
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 300
Info: LANGEVIN USING BBK INTEGRATOR
Info: LANGEVIN DAMPING COEFFICIENT IS 1 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 300 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ISOTROPIC
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 112 108 96
Info: PME MAXIMUM GRID SPACING 1
Info: Attempting to read FFTW data from FFTW_NAMD_2.12_Linux-x86_64-multicore.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.12_Linux-x86_64-multicore.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
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-05
Info: MAX ITERATIONS : 100
Info: RIGID WATER USING SETTLE ALGORITHM
Info: RANDOM NUMBER SEED 1589474687
Info: USE HYDROGEN BONDS? NO
Info: Using AMBER format force field!
Info: AMBER PARM FILE ./t1y_water.prmtop
Info: AMBER COORDINATE FILE ./t1y_water.inpcrd
Info: Exclusions will be read from PARM file!
Info: SCNB (VDW SCALING) 2
Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
Reading parm file (./t1y_water.prmtop) ...
PARM file in AMBER 7 format
Warning: Skipping ATOMIC_NUMBER in parm file while seeking MASS.
Warning: Skipping SCEE_SCALE_FACTOR in parm file while seeking SOLTY.
Warning: Skipping SCNB_SCALE_FACTOR in parm file while seeking SOLTY.
Warning: Encounter 10-12 H-bond term
Warning: Found 28843 H-H bonds.
Info: SUMMARY OF PARAMETERS:
Info: 44 BONDS
Info: 92 ANGLES
Info: 92 HARMONIC
Info: 0 COSINE-BASED
Info: 48 DIHEDRAL
Info: 0 IMPROPER
Info: 0 CROSSTERM
Info: 0 VDW
Info: 153 VDW_PAIRS
Info: 0 NBTHOLE_PAIRS
Info: TIME FOR READING PDB FILE: 1.69277e-05
Info:
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 95737 ATOMS
Info: 95829 BONDS
Info: 16841 ANGLES
Info: 35533 DIHEDRALS
Info: 0 IMPROPERS
Info: 0 CROSSTERMS
Info: 136921 EXCLUSIONS
Info: 91126 RIGID BONDS
Info: 196085 DEGREES OF FREEDOM
Info: 33454 HYDROGEN GROUPS
Info: 4 ATOMS IN LARGEST HYDROGEN GROUP
Info: 33454 MIGRATION GROUPS
Info: 4 ATOMS IN LARGEST MIGRATION GROUP
Info: TOTAL MASS = 585252 amu
Info: TOTAL CHARGE = -1.68988e-06 e
Info: MASS DENSITY = 0.901472 g/cm^3
Info: ATOM DENSITY = 0.0888035 atoms/A^3
Info: *****************************
Info:
Info: Entering startup at 8.21327 s, 2471.26 MB of memory in use
Info: Startup phase 0 took 0.000333071 s, 2471.26 MB of memory in use
Info: ADDED 0 IMPLICIT EXCLUSIONS
Info: Startup phase 1 took 0.0468209 s, 2482.88 MB of memory in use
Info: NONBONDED TABLE R-SQUARED SPACING: 0.0625
Info: NONBONDED TABLE SIZE: 705 POINTS
Info: INCONSISTENCY IN FAST TABLE ENERGY VS FORCE: 0.000290479 AT 0.251946
Info: INCONSISTENCY IN SCOR TABLE ENERGY VS FORCE: 0.000178193 AT 9.97184
Info: ABSOLUTE IMPRECISION IN VDWA TABLE FORCE: 1.00974e-28 AT 9.99687
Info: INCONSISTENCY IN VDWA TABLE ENERGY VS FORCE: 0.0040507 AT 0.251946
Info: ABSOLUTE IMPRECISION IN VDWB TABLE FORCE: 6.2204e-22 AT 9.99687
Info: INCONSISTENCY IN VDWB TABLE ENERGY VS FORCE: 0.00150189 AT 0.251946
Info: Startup phase 2 took 0.00110817 s, 2482.88 MB of memory in use
Info: Startup phase 3 took 0.000199795 s, 2482.88 MB of memory in use
Info: Startup phase 4 took 0.00692105 s, 2482.88 MB of memory in use
Info: Startup phase 5 took 0.000262022 s, 2482.88 MB of memory in use
Info: PATCH GRID IS 6 (PERIODIC) BY 5 (PERIODIC) BY 5 (PERIODIC)
Info: PATCH GRID IS 1-AWAY BY 1-AWAY BY 1-AWAY
Info: REMOVING COM VELOCITY 0.00743926 0.0386896 -0.0070714
Info: LARGEST PATCH (68) HAS 716 ATOMS
Info: TORUS A SIZE 32 USING 0
Info: TORUS B SIZE 1 USING 0
Info: TORUS C SIZE 1 USING 0
Info: TORUS MINIMAL MESH SIZE IS 1 BY 1 BY 1
Info: Placed 100% of base nodes on same physical node as patch
Info: Startup phase 6 took 0.0348861 s, 2499.81 MB of memory in use
Info: PME using 28 and 27 processors for FFT and reciprocal sum.
Info: PME GRID LOCATIONS: 1 2 3 4 5 6 7 9 10 11 ...
Info: PME TRANS LOCATIONS: 1 2 3 4 5 6 8 9 10 11 ...
Info: PME USING 1 GRID NODES AND 1 TRANS NODES
Info: Startup phase 7 took 0.00529599 s, 2499.81 MB of memory in use
Info: Startup phase 8 took 0.00334787 s, 2499.81 MB of memory in use
LDB: Central LB being created...
Info: Startup phase 9 took 0.00493598 s, 2499.81 MB of memory in use
Info: CREATING 3160 COMPUTE OBJECTS
Info: useSync: 0 useProxySync: 0
Info: Startup phase 10 took 0.056572 s, 2499.81 MB of memory in use
Info: Startup phase 11 took 0.000294209 s, 2499.81 MB of memory in use
Info: Startup phase 12 took 0.000485897 s, 2499.81 MB of memory in use
Info: Finished startup at 8.37473 s, 2499.81 MB of memory in use
TCL: Minimizing for 30000 steps
Warning: Bad global bond count! (95828 vs 95829)
Warning: Bad global angle count! (16837 vs 16841)
Warning: Bad global dihedral count! (35510 vs 35533)
Warning: Low global exclusion count! (136877 vs 136921)
Warning: This warning is not unusual during minimization.
Warning: Increasing pairlistdist or cutoff may avoid this.
PRESSURE: 0 9.37973e+10 4.06414e+10 1.31199e+11 4.06414e+10 1.76223e+10 5.6857e+10 1.31199e+11 5.6857e+10 1.83529e+11
GPRESSURE: 0 -7.21723e+11 9.71225e+10 6.12946e+11 -3.12813e+11 4.21002e+10 2.6565e+11 -1.00962e+12 1.35868e+11 8.5744e+11
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT VDW BOUNDARY MISC KINETIC TOTAL TEMP POTENTIAL TOTAL3 TEMPAVG PRESSURE GPRESSURE VOLUME PRESSAVG GPRESSAVG
ENERGY: 0 183919.9152 2235.4803 5958.9706 0.0000 -298978.4694 9999999999.9999 0.0000 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 1078077.0000 9999999999.9999 9999999999.9999
OPENING EXTENDED SYSTEM TRAJECTORY FILE
MINIMIZER SLOWLY MOVING 69 ATOMS WITH BAD CONTACTS DOWNHILL
Warning: Bad global bond count! (95828 vs 95829)
Warning: Bad global angle count! (16837 vs 16841)
Warning: Bad global dihedral count! (35510 vs 35533)
Warning: Low global exclusion count! (136877 vs 136921)
Warning: This warning is not unusual during minimization.
Warning: Increasing pairlistdist or cutoff may avoid this.
PRESSURE: 1 6.41534e+09 6.67329e+09 2.45262e+10 6.67329e+09 6.94536e+09 2.55174e+10 2.45262e+10 2.55174e+10 9.37826e+10
GPRESSURE: 1 -7.12037e+10 1.20488e+10 7.03779e+10 -7.40848e+10 1.25376e+10 7.32207e+10 -2.72266e+11 4.60726e+10 2.69106e+11
ENERGY: 1 178329.3651 2218.5431 5963.1686 0.0000 -298941.8018 9999999999.9999 0.0000 0.0000 0.0000 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 0.0000 9999999999.9999 9999999999.9999 1078077.0000 9999999999.9999 9999999999.9999
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发表于 Post on 2020-5-16 22:39:32
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