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bay__gulf金虫 (著名写手)
刘苏州
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【在线答疑】关于NAMD/VMD已有27人参与
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小木虫(金币+0.5):给个红包，谢谢回帖交流
小木虫(金币+0.5):给个红包，谢谢回帖交流
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运行NAMD出现如下错误,原因是什么? Charm++: standalone mode (not using charmrun) Info: NAMD 2.6 for Linux-i686 Info: Info: Please visit http://www.ks.uiuc.edu/Research/namd/ Info: and send feedback or bug reports to namd@ks.uiuc.edu Info: 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 50900 for net-linux-iccstatic Info: Built Wed Aug 30 12:54:30 CDT 2006 by jim on kyoto.ks.uiuc.edu Info: 1 NAMD 2.6 Linux-i686 1 Info: Running on 1 processors. Info: 7240 kB of memory in use. Info: Memory usage based on mallinfo Info: Configuration file is rgbiw.namd TCL: Suspending until startup complete. Info: SIMULATION PARAMETERS: Info: TIMESTEP 1 Info: NUMBER OF STEPS 0 Info: STEPS PER CYCLE 20 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: 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 298 Info: CENTER OF MASS MOVING INITIALLY? NO Info: DIELECTRIC 1 Info: EXCLUDE SCALED ONE-FOUR Info: 1-4 SCALE FACTOR 1 Info: DCD FILENAME rgbinw.dcd Info: DCD FREQUENCY 50 Info: DCD FIRST STEP 50 Info: XST FILENAME rgbinw.xst Info: XST FREQUENCY 50 Info: NO VELOCITY DCD OUTPUT Info: OUTPUT FILENAME rgbinw Info: RESTART FILENAME rgbinw.restart Info: RESTART FREQUENCY 1000 Info: SWITCHING ACTIVE Info: SWITCHING ON 9 Info: SWITCHING OFF 10 Info: PAIRLIST DISTANCE 12 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 0 Info: HYDROGEN GROUP CUTOFF 2.5 Info: PATCH DIMENSION 14.5 Info: ENERGY OUTPUT STEPS 100 Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL Info: TIMING OUTPUT STEPS 1000 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 1249824237 Info: USE HYDROGEN BONDS? NO Info: COORDINATE PDB rgbinro1aw.pdb Info: STRUCTURE FILE rgbinro1aw.psf Info: PARAMETER file: CHARMM format! Info: PARAMETERS par_all27_prot_lipid_na.inp Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS Warning: DUPLICATE ANGLE ENTRY FOR CPH1-NR1-CPH2 PREVIOUS VALUES k=130 theta0=107.5 k_ub=0 r_ub=0 USING VALUES k=130 theta0=107 k_ub=0 r_ub=0 Info: SUMMARY OF PARAMETERS: Info: 299 BONDS Info: 729 ANGLES Info: 1145 DIHEDRAL Info: 84 IMPROPER Info: 0 CROSSTERM Info: 161 VDW Info: 0 VDW_PAIRS FATAL ERROR: CAN'T FIND CROSSTERM PARAMETERS FOR C NH1 CT1 C NH1 CT1 C NH1 Stack Traceback: [0] _ZN10Parameters22assign_crossterm_indexEPcS0_S0_S0_S0_S0_S0_S0_P9crossterm+0x34b [0x828a447] [1] _ZN8Molecule15read_crosstermsEP8_IO_FILEP10Parameters+0x29f [0x8265027] [2] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x1129 [0x8262fed] [3] _ZN8MoleculeC9EP13SimParametersP10ParametersPc+0x246 [0x8261e02] [4] _ZN8MoleculeC1EP13SimParametersP10ParametersPc+0x14 [0x82665d0] [5] _ZN9NamdState14configListInitEP10ConfigList+0x49b [0x827abc7] [6] _ZN9ScriptTcl9initcheckEv+0x5e [0x82b9f8e] [7] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e [0x82b74a2] [8] TclInvokeStringCommand+0x7f [0x8395d58] [9] namd2 [0x83ca7c1] [10] Tcl_EvalEx+0x1c3 [0x83cae4e] [11] Tcl_EvalFile+0x138 [0x83c2afa] [12] _ZN9ScriptTcl3runEPc+0x1a [0x82b6a86] [13] main+0x1d6 [0x80df19a] [14] __libc_start_main+0xbc [0x4012dbac] [15] _ZStlsISt11char_traitsIcEERSt13basic_ostreamIcT_ES5_c+0x59 [0x80dba71] |
43楼2009-08-11 11:50:27
2楼2009-05-02 11:58:42
bay__gulf
金虫 (著名写手)
刘苏州
- 模拟EPI: 8
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- 注册: 2008-09-03
- 专业: 理论和计算化学
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lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
lei0736(金币+4,VIP+0):谢谢 又添猛将 5-3 16:09
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【回2楼】 可以，比如下面这篇文献 Bryan J. Johnson, Jordi Cohen, Richard W. Welford, Arwen R. Pearson, Klaus Schulten, Judith P. Klinman, and Carrie M. Wilmot. Exploring molecular oxygen pathways in Hanseluna Polymorpha copper-containing amine oxidase. Journal of Biological Chemistry, 282:17767-17776, 2007. [ Last edited by bay__gulf on 2009-5-2 at 13:21 ] |
3楼2009-05-02 13:13:06
4楼2009-05-02 13:45:28