| 查看: 2149 | 回复: 6 | |||
[求助]
用oniom方法优化六肽的二聚体，结果报错 求指导
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我用GV画的分子，输入文件如下： %chk=02.chk %mem=8000MB %nprocshared=8 # opt freq oniom(b3lyp/3-21g:am1)=(EmbedCharge,Svalue) geom=connectivity opt freq 02 0 1 0 1 0 1 ....（分子坐标我就不写了） 运行一段时间后报错，错误如下：（tail log文件 结果如下） Using GEDIIS/GDIIS optimizer. Bend failed for angle 47 - 48 - 125 Tors failed for dihedral 45 - 47 - 48 - 125 Tors failed for dihedral 49 - 47 - 48 - 125 Tors failed for dihedral 62 - 47 - 48 - 125 Tors failed for dihedral 47 - 48 - 125 - 124 FormBX had a problem. Error termination via Lnk1e in /home/zhangjin/software/g09/l103.exe at Wed Oct 9 04:42:02 2013. Job cpu time: 2 days 9 hours 23 minutes 10.0 seconds. File lengths (MBytes): RWF= 614 Int= 0 D2E= 0 Chk= 126 Scr= 1 求高手指教~~ |
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2楼2013-10-09 11:53:46
3楼2013-10-10 16:49:04
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%chk=02.chk %mem=8000MB %nprocshared=8 # opt freq oniom(b3lyp/3-21g:am1)=(EmbedCharge,Svalue) geom=connectivity opt freq 02 0 1 0 1 0 1 C(PDBName=CA,ResName=GLY,ResNum=1) 0 -10.17500000 -0.43700000 -2.25200000 L H(PDBName=HA1,ResName=GLY,ResNum=1) 0 -10.03200000 -1.20800000 -2.99700000 L H(PDBName=HA2,ResName=GLY,ResNum=1) 0 -10.30300000 -0.79200000 -1.23800000 L C(PDBName=C,ResName=GLY,ResNum=1) 0 -9.01400000 0.49900000 -2.29400000 L O(PDBName=O,ResName=GLY,ResNum=1) 0 -9.27300000 1.67700000 -2.52700000 L N(PDBName=N,ResName=GLY,ResNum=2) 0 -7.77400000 0.03700000 -2.10800000 L H(PDBName=HN,ResName=GLY,ResNum=2) 0 -7.54300000 -0.91300000 -1.87400000 L C(PDBName=CA,ResName=GLY,ResNum=2) 0 -6.58900000 0.87000000 -2.25200000 L H(PDBName=HA1,ResName=GLY,ResNum=2) 0 -6.58000000 1.63500000 -1.48900000 L H(PDBName=HA2,ResName=GLY,ResNum=2) 0 -6.52200000 1.23900000 -3.26700000 L C(PDBName=C,ResName=GLY,ResNum=2) 0 -5.43400000 -0.04400000 -2.00700000 L O(PDBName=O,ResName=GLY,ResNum=2) 0 -5.60200000 -1.00600000 -1.26400000 L N(PDBName=N,ResName=VAL,ResNum=3) 0 -4.28600000 0.21100000 -2.64800000 L H(PDBName=HN,ResName=VAL,ResNum=3) 0 -4.14800000 1.03200000 -3.20100000 L C(PDBName=CA,ResName=VAL,ResNum=3) 0 -3.09400000 -0.61800000 -2.60400000 L H 17 H(PDBName=HA,ResName=VAL,ResNum=3) 0 -3.04900000 -1.15600000 -1.67400000 L C(PDBName=CB,ResName=VAL,ResNum=3) 0 -2.97200000 -1.60400000 -3.77500000 H H(PDBName=HB,ResName=VAL,ResNum=3) 0 -2.92000000 -1.04000000 -4.73700000 H C(PDBName=CG1,ResName=VAL,ResNum=3) 0 -1.70300000 -2.47400000 -3.63800000 H H(PDBName=HG11,ResName=VAL,ResNum=3) 0 -1.68400000 -3.24700000 -4.43600000 H H(PDBName=HG12,ResName=VAL,ResNum=3) 0 -0.77600000 -1.87100000 -3.73900000 H H(PDBName=HG13,ResName=VAL,ResNum=3) 0 -1.68500000 -2.99300000 -2.65700000 H C(PDBName=CG2,ResName=VAL,ResNum=3) 0 -4.19900000 -2.53600000 -3.82300000 H H(PDBName=HG21,ResName=VAL,ResNum=3) 0 -4.06100000 -3.30500000 -4.61300000 H H(PDBName=HG22,ResName=VAL,ResNum=3) 0 -4.32500000 -3.05600000 -2.84900000 H H(PDBName=HG23,ResName=VAL,ResNum=3) 0 -5.12400000 -1.97000000 -4.05200000 H C(PDBName=C,ResName=VAL,ResNum=3) 0 -1.96100000 0.38800000 -2.65400000 L O(PDBName=O,ResName=VAL,ResNum=3) 0 -2.12100000 1.43900000 -3.27200000 L N(PDBName=N,ResName=VAL,ResNum=4) 0 -0.82200000 0.12400000 -1.99200000 L H(PDBName=HN,ResName=VAL,ResNum=4) 0 -0.67400000 -0.74400000 -1.52200000 L C(PDBName=CA,ResName=VAL,ResNum=4) 0 0.36300000 0.96400000 -2.04100000 L H 33 H(PDBName=HA,ResName=VAL,ResNum=4) 0 0.34300000 1.60200000 -2.91300000 L C(PDBName=CB,ResName=VAL,ResNum=4) 0 0.53300000 1.80300000 -0.76600000 H H(PDBName=HB,ResName=VAL,ResNum=4) 0 0.46100000 1.12000000 0.11100000 H C(PDBName=CG1,ResName=VAL,ResNum=4) 0 1.87900000 2.55600000 -0.69500000 H H(PDBName=HG11,ResName=VAL,ResNum=4) 0 1.89700000 3.22600000 0.19000000 H H(PDBName=HG12,ResName=VAL,ResNum=4) 0 2.73900000 1.86000000 -0.59500000 H H(PDBName=HG13,ResName=VAL,ResNum=4) 0 2.03100000 3.18000000 -1.60100000 H C(PDBName=CG2,ResName=VAL,ResNum=4) 0 -0.60700000 2.83600000 -0.68500000 H H(PDBName=HG21,ResName=VAL,ResNum=4) 0 -0.49900000 3.45500000 0.23100000 H H(PDBName=HG22,ResName=VAL,ResNum=4) 0 -0.59100000 3.50500000 -1.57100000 H H(PDBName=HG23,ResName=VAL,ResNum=4) 0 -1.59600000 2.33600000 -0.64000000 H C(PDBName=C,ResName=VAL,ResNum=4) 0 1.50300000 -0.02200000 -2.21700000 L O(PDBName=O,ResName=VAL,ResNum=4) 0 1.36000000 -1.18800000 -1.85000000 L N(PDBName=N,ResName=ILE,ResNum=5) 0 2.63100000 0.41300000 -2.80600000 L H(PDBName=HN,ResName=ILE,ResNum=5) 0 2.75100000 1.36300000 -3.08500000 L C(PDBName=CA,ResName=ILE,ResNum=5) 0 3.85800000 -0.34700000 -2.93400000 L H 49 H(PDBName=HA,ResName=ILE,ResNum=5) 0 3.97000000 -0.98000000 -2.07800000 L C(PDBName=CB,ResName=ILE,ResNum=5) 0 3.90900000 -1.26500000 -4.15700000 H H(PDBName=HB,ResName=ILE,ResNum=5) 0 2.96000000 -1.85100000 -4.14900000 H C(PDBName=CG2,ResName=ILE,ResNum=5) 0 3.96600000 -0.45400000 -5.46900000 H H(PDBName=HG21,ResName=ILE,ResNum=5) 0 3.90700000 -1.13400000 -6.34300000 H H(PDBName=HG22,ResName=ILE,ResNum=5) 0 3.12700000 0.26900000 -5.52400000 H H(PDBName=HG23,ResName=ILE,ResNum=5) 0 4.92500000 0.10600000 -5.53400000 H C(PDBName=CG1,ResName=ILE,ResNum=5) 0 5.06600000 -2.28800000 -4.03600000 H H(PDBName=HG11,ResName=ILE,ResNum=5) 0 6.03500000 -1.77600000 -4.24300000 H H(PDBName=HG12,ResName=ILE,ResNum=5) 0 5.11800000 -2.65400000 -2.98500000 H C(PDBName=CD,ResName=ILE,ResNum=5) 0 4.92200000 -3.50200000 -4.96100000 H H(PDBName=HD1,ResName=ILE,ResNum=5) 0 5.77500000 -4.19700000 -4.79700000 H H(PDBName=HD2,ResName=ILE,ResNum=5) 0 3.97700000 -4.04400000 -4.74800000 H H(PDBName=HD3,ResName=ILE,ResNum=5) 0 4.93000000 -3.18600000 -6.02500000 H C(PDBName=C,ResName=ILE,ResNum=5) 0 4.97300000 0.68100000 -2.85800000 L O(PDBName=O,ResName=ILE,ResNum=5) 0 4.73100000 1.85600000 -3.14700000 L N(PDBName=N,ResName=ALA,ResNum=6) 0 6.16900000 0.27600000 -2.41500000 L H(PDBName=HN,ResName=ALA,ResNum=6) 0 6.41700000 -0.67800000 -2.25500000 L C(PDBName=CA,ResName=ALA,ResNum=6) 0 7.37100000 1.06000000 -2.40400000 L H 68 H(PDBName=HA,ResName=ALA,ResNum=6) 0 7.29400000 1.87700000 -3.10600000 L C(PDBName=CB,ResName=ALA,ResNum=6) 0 7.68400000 1.56500000 -0.98300000 H H(PDBName=HB1,ResName=ALA,ResNum=6) 0 6.87000000 2.22300000 -0.61900000 H H(PDBName=HB2,ResName=ALA,ResNum=6) 0 7.78600000 0.70300000 -0.28900000 H H(PDBName=HB3,ResName=ALA,ResNum=6) 0 8.64100000 2.12800000 -0.98200000 H C(PDBName=C,ResName=ALA,ResNum=6) 0 8.49300000 0.11700000 -2.91700000 L O(PDBName=OT1,ResName=ALA,ResNum=6) 0 8.29421645 -1.12426279 -2.97463981 L C(PDBName=CA,ResName=GLY,ResNum=1) 0 -10.13100000 -0.39400000 3.19000000 L H(PDBName=HA1,ResName=GLY,ResNum=1) 0 -10.36900000 -1.25900000 2.58500000 L H(PDBName=HA2,ResName=GLY,ResNum=1) 0 -9.82400000 -0.61900000 4.20200000 L C(PDBName=C,ResName=GLY,ResNum=1) 0 -9.04500000 0.38100000 2.52200000 L O(PDBName=O,ResName=GLY,ResNum=1) 0 -9.38900000 1.36900000 1.87300000 L N(PDBName=N,ResName=GLY,ResNum=2) 0 -7.77600000 -0.01200000 2.67700000 L H(PDBName=HN,ResName=GLY,ResNum=2) 0 -7.49600000 -0.82100000 3.20900000 L C(PDBName=CA,ResName=GLY,ResNum=2) 0 -6.60400000 0.69700000 2.18800000 L H(PDBName=HA1,ResName=GLY,ResNum=2) 0 -6.50400000 1.64200000 2.70500000 L H(PDBName=HA2,ResName=GLY,ResNum=2) 0 -6.62500000 0.75500000 1.11000000 L C(PDBName=C,ResName=GLY,ResNum=2) 0 -5.45800000 -0.17800000 2.59100000 L O(PDBName=O,ResName=GLY,ResNum=2) 0 -5.68700000 -1.12600000 3.33800000 L N(PDBName=N,ResName=VAL,ResNum=3) 0 -4.24400000 0.09600000 2.10300000 L H(PDBName=HN,ResName=VAL,ResNum=3) 0 -4.04900000 0.91100000 1.55800000 L C(PDBName=CA,ResName=VAL,ResNum=3) 0 -3.05200000 -0.70400000 2.33500000 L H 90 H(PDBName=HA,ResName=VAL,ResNum=3) 0 -3.09200000 -1.17500000 3.30800000 L C(PDBName=CB,ResName=VAL,ResNum=3) 0 -2.79200000 -1.72700000 1.21800000 H H(PDBName=HB,ResName=VAL,ResNum=3) 0 -2.75400000 -1.17400000 0.25600000 H C(PDBName=CG1,ResName=VAL,ResNum=3) 0 -1.45900000 -2.48700000 1.38800000 H H(PDBName=HG11,ResName=VAL,ResNum=3) 0 -1.36900000 -3.27200000 0.60700000 H H(PDBName=HG12,ResName=VAL,ResNum=3) 0 -0.58000000 -1.81800000 1.27900000 H H(PDBName=HG13,ResName=VAL,ResNum=3) 0 -1.41100000 -2.98500000 2.38000000 H C(PDBName=CG2,ResName=VAL,ResNum=3) 0 -3.93700000 -2.75600000 1.14200000 H H(PDBName=HG21,ResName=VAL,ResNum=3) 0 -3.72000000 -3.51000000 0.35500000 H H(PDBName=HG22,ResName=VAL,ResNum=3) 0 -4.04700000 -3.28400000 2.11300000 H H(PDBName=HG23,ResName=VAL,ResNum=3) 0 -4.89900000 -2.26900000 0.88900000 H C(PDBName=C,ResName=VAL,ResNum=3) 0 -1.94600000 0.33000000 2.33600000 L O(PDBName=O,ResName=VAL,ResNum=3) 0 -2.10100000 1.36900000 1.69700000 L N(PDBName=N,ResName=VAL,ResNum=4) 0 -0.84000000 0.09600000 3.06400000 L H(PDBName=HN,ResName=VAL,ResNum=4) 0 -0.71500000 -0.76300000 3.55800000 L C(PDBName=CA,ResName=VAL,ResNum=4) 0 0.33700000 0.94600000 3.10100000 L H 106 H(PDBName=HA,ResName=VAL,ResNum=4) 0 0.42500000 1.49900000 2.17800000 L C(PDBName=CB,ResName=VAL,ResNum=4) 0 0.37800000 1.90500000 4.30200000 H H(PDBName=HB,ResName=VAL,ResNum=4) 0 0.41700000 1.31600000 5.24800000 H C(PDBName=CG1,ResName=VAL,ResNum=4) 0 1.61100000 2.83300000 4.23600000 H H(PDBName=HG11,ResName=VAL,ResNum=4) 0 1.55800000 3.59500000 5.04200000 H H(PDBName=HG12,ResName=VAL,ResNum=4) 0 2.55800000 2.27000000 4.37300000 H H(PDBName=HG13,ResName=VAL,ResNum=4) 0 1.65000000 3.36300000 3.26000000 H C(PDBName=CG2,ResName=VAL,ResNum=4) 0 -0.89100000 2.78000000 4.33100000 H H(PDBName=HG21,ResName=VAL,ResNum=4) 0 -0.82200000 3.52900000 5.14700000 H H(PDBName=HG22,ResName=VAL,ResNum=4) 0 -1.00800000 3.31900000 3.36600000 H H(PDBName=HG23,ResName=VAL,ResNum=4) 0 -1.79600000 2.16300000 4.50300000 H C(PDBName=C,ResName=VAL,ResNum=4) 0 1.48700000 -0.04500000 3.18400000 L O(PDBName=O,ResName=VAL,ResNum=4) 0 1.29700000 -1.15000000 3.69100000 L N(PDBName=N,ResName=ILE,ResNum=5) 0 2.67400000 0.30100000 2.66900000 L H(PDBName=HN,ResName=ILE,ResNum=5) 0 2.84300000 1.18500000 2.23200000 L C(PDBName=CA,ResName=ILE,ResNum=5) 0 3.88500000 -0.49100000 2.75900000 L H 122 H(PDBName=HA,ResName=ILE,ResNum=5) 0 4.00000000 -0.84900000 3.77100000 L C(PDBName=CB,ResName=ILE,ResNum=5) 0 3.89500000 -1.67800000 1.79000000 H H(PDBName=HB,ResName=ILE,ResNum=5) 0 3.03300000 -2.33100000 2.06800000 H C(PDBName=CG2,ResName=ILE,ResNum=5) 0 3.64500000 -1.15400000 0.37400000 H H(PDBName=HG21,ResName=ILE,ResNum=5) 0 3.50800000 -2.00300000 -0.32700000 H H(PDBName=HG22,ResName=ILE,ResNum=5) 0 2.73000000 -0.53200000 0.31400000 H H(PDBName=HG23,ResName=ILE,ResNum=5) 0 4.51100000 -0.54600000 0.03000000 H C(PDBName=CG1,ResName=ILE,ResNum=5) 0 5.16800000 -2.55900000 1.85700000 H H(PDBName=HG11,ResName=ILE,ResNum=5) 0 6.05600000 -1.95300000 1.55800000 H H(PDBName=HG12,ResName=ILE,ResNum=5) 0 5.33200000 -2.88600000 2.90700000 H C(PDBName=CD,ResName=ILE,ResNum=5) 0 5.11500000 -3.79100000 0.94200000 H H(PDBName=HD1,ResName=ILE,ResNum=5) 0 6.01800000 -4.42000000 1.10200000 H H(PDBName=HD2,ResName=ILE,ResNum=5) 0 4.20900000 -4.39800000 1.14500000 H H(PDBName=HD3,ResName=ILE,ResNum=5) 0 5.11100000 -3.48200000 -0.12600000 H C(PDBName=C,ResName=ILE,ResNum=5) 0 4.99100000 0.52500000 2.51600000 L O(PDBName=O,ResName=ILE,ResNum=5) 0 4.70700000 1.61300000 2.00600000 L N(PDBName=N,ResName=ALA,ResNum=6) 0 6.21400000 0.21900000 2.96100000 L H(PDBName=HN,ResName=ALA,ResNum=6) 0 6.48000000 -0.67000000 3.34700000 L C(PDBName=CA,ResName=ALA,ResNum=6) 0 7.40300000 1.01700000 2.94100000 L H 141 H(PDBName=HA,ResName=ALA,ResNum=6) 0 7.65300000 1.29200000 1.92500000 L C(PDBName=CB,ResName=ALA,ResNum=6) 0 7.28000000 2.23900000 3.87700000 H H(PDBName=HB1,ResName=ALA,ResNum=6) 0 6.47500000 2.91300000 3.52500000 H H(PDBName=HB2,ResName=ALA,ResNum=6) 0 7.05200000 1.89300000 4.90700000 H H(PDBName=HB3,ResName=ALA,ResNum=6) 0 8.24500000 2.78900000 3.89300000 H C(PDBName=C,ResName=ALA,ResNum=6) 0 8.50900000 0.07100000 3.48400000 L O(PDBName=OT1,ResName=ALA,ResNum=6) 0 8.21434245 -1.09613840 3.85079073 L O 0 -11.36600000 0.42100000 -2.63400000 L C 0 -12.56091819 -0.22209203 -2.63762646 L O 0 -12.54681224 -1.45227228 -2.64203094 L O 0 -11.26237668 0.47891155 3.24396525 L C 0 -12.37886006 -0.20747123 3.59575147 L O 0 -12.26423896 -1.41420686 3.80602017 L N 0 9.78735543 0.67428592 -3.33530184 L H 0 10.11105042 0.19111849 -4.14879479 L N 0 9.89983551 0.53917288 3.56938583 L H 0 10.45329602 0.06667964 2.88350566 L C 0 10.76425993 0.51343815 -2.24870826 L H 0 11.72911417 0.30943327 -2.66384475 L H 0 10.80730434 1.41347239 -1.67165925 L H 0 10.46744110 -0.29967084 -1.61969924 L C 0 10.43160978 0.25347370 4.90971866 L H 0 10.61612189 -0.79627890 5.00392458 L H 0 11.34595463 0.79055505 5.05260718 L H 0 9.71982641 0.55818716 5.64824025 L C 0 -13.75064894 0.75572983 -2.63535628 L H 0 -13.68151886 1.40353627 -3.48416005 L H 0 -14.66609827 0.20372022 -2.68159378 L H 0 -13.73096043 1.33932845 -1.73873762 L C 0 -13.62309625 0.69727981 3.66576475 L H 0 -13.83601416 1.08689658 2.69223266 L H 0 -14.45955172 0.12721924 4.01256903 L H 0 -13.43822426 1.50634909 4.34113817 L 1 2 1.0 3 1.0 4 1.0 147 1.0 2 3 4 5 2.0 6 1.5 5 6 7 1.0 8 1.0 7 8 9 1.0 10 1.0 11 1.0 9 10 11 12 2.0 13 1.5 12 13 14 1.0 15 1.0 14 15 17 1.0 16 1.0 27 1.0 16 17 23 1.0 19 1.0 18 1.0 18 19 20 1.0 21 1.0 22 1.0 20 21 22 23 24 1.0 26 1.0 25 1.0 24 25 26 27 28 2.0 29 1.5 28 29 30 1.0 31 1.0 30 31 32 1.0 33 1.0 43 1.0 32 33 34 1.0 35 1.0 39 1.0 34 35 36 1.0 37 1.0 38 1.0 36 37 38 39 40 1.0 41 1.0 42 1.0 40 41 42 43 44 2.0 45 1.5 44 45 46 1.0 47 1.0 46 47 49 1.0 48 1.0 62 1.0 48 49 50 1.0 55 1.0 51 1.0 50 51 52 1.0 53 1.0 54 1.0 52 53 54 55 56 1.0 58 1.0 57 1.0 56 57 58 59 1.0 60 1.0 61 1.0 59 60 61 62 63 2.0 64 1.5 63 64 65 1.0 66 1.0 65 66 67 1.0 68 1.0 72 1.0 67 68 69 1.0 70 1.0 71 1.0 69 70 71 72 73 2.0 153 1.0 73 74 75 1.0 76 1.0 77 1.0 150 1.0 75 76 77 78 2.0 79 1.5 78 79 81 1.0 80 1.0 80 81 83 1.0 84 1.0 82 1.0 82 83 84 86 1.5 85 2.0 85 86 87 1.0 88 1.0 87 88 90 1.0 100 1.0 89 1.0 89 90 96 1.0 92 1.0 91 1.0 91 92 93 1.0 94 1.0 95 1.0 93 94 95 96 97 1.0 98 1.0 99 1.0 97 98 99 100 101 2.0 102 1.5 101 102 103 1.0 104 1.0 103 104 105 1.0 106 1.0 116 1.0 105 106 107 1.0 108 1.0 112 1.0 107 108 109 1.0 110 1.0 111 1.0 109 110 111 112 113 1.0 114 1.0 115 1.0 113 114 115 116 117 2.0 118 1.5 117 118 119 1.0 120 1.0 119 120 122 1.0 135 1.0 121 1.0 121 122 123 1.0 128 1.0 124 1.0 123 124 126 1.0 125 1.0 127 1.0 125 126 127 128 129 1.0 131 1.0 130 1.0 129 130 131 132 1.0 133 1.0 134 1.0 132 133 134 135 136 2.0 137 1.5 136 137 138 1.0 139 1.0 138 139 140 1.0 141 1.0 145 1.0 140 141 142 1.0 143 1.0 144 1.0 142 143 144 145 146 2.0 155 1.0 146 147 148 1.0 148 149 2.0 165 1.0 149 150 151 1.0 151 152 2.0 169 1.0 152 153 154 1.0 157 1.0 154 155 156 1.0 161 1.0 156 157 158 1.0 159 1.0 160 1.0 158 159 160 161 162 1.0 163 1.0 164 1.0 162 163 164 165 166 1.0 167 1.0 168 1.0 166 167 168 169 170 1.0 171 1.0 172 1.0 170 171 172 麻烦你了~~ 这是输入文件 |
4楼2013-10-10 16:52:06
枪下游魂
木虫 (著名写手)
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5楼2013-10-11 07:12:48
6楼2013-10-11 10:06:09
7楼2014-10-23 16:56:17
