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29050801新虫 (小有名气)
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[求助]
MOPAC结构优化如何得到分子结构文件 已有1人参与
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用MOPAC做了结构优化 请问如何利用得到的输出文件转换成分子的结构文件呢？ 用的MOPAC2012 已经通过注册了 |
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jerkwin
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5楼2014-01-09 09:21:46
jerkwin
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2楼2014-01-08 21:31:09
29050801
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这下面是输出的坐标部分 -------- C -5.97505740 +1 0.98208664 +1 0.26296428 +1 0.2825 C -6.01839866 +1 2.00213620 +1 -0.89584916 +1 0.0706 C -4.67415747 +1 2.73759833 +1 -0.96482207 +1 0.0754 C -4.40605110 +1 3.37640234 +1 0.41725809 +1 0.0217 C -4.36610784 +1 2.27665190 +1 1.49224149 +1 0.0346 C -4.25842649 +1 2.83801030 +1 2.91467263 +1 -0.0245 C -4.39874216 +1 -4.00038337 +1 -0.12338527 +1 0.2855 C -5.48651111 +1 -3.43111983 +1 -1.06784780 +1 0.0508 C -5.27960185 +1 -1.91877490 +1 -1.22104601 +1 0.0747 C -5.26343986 +1 -1.28843902 +1 0.18821640 +1 0.0213 C -4.12231024 +1 -1.91281051 +1 1.00794275 +1 0.0356 C -4.05362804 +1 -1.45694906 +1 2.47629031 +1 -0.0103 C 0.22420073 +1 -5.95117202 +1 -1.51047187 +1 0.2910 C -0.68045832 +1 -5.63692395 +1 -2.72610876 +1 0.0632 C -1.65035507 +1 -4.50326881 +1 -2.35903763 +1 0.0776 C -2.41953404 +1 -4.92047534 +1 -1.08735670 +1 0.0330 C -1.43302115 +1 -5.24699280 +1 0.04985434 +1 0.0313 C -2.12617834 +1 -5.85923213 +1 1.27211827 +1 -0.0268 C 4.75113430 +1 -3.47924139 +1 -0.49889190 +1 0.2941 C 4.49398521 +1 -4.12205271 +1 -1.88476263 +1 0.0495 C 2.98397409 +1 -4.15362915 +1 -2.15661704 +1 0.0767 C 2.30091155 +1 -4.89772682 +1 -0.98959988 +1 0.0169 C 2.61824226 +1 -4.17430968 +1 0.33091319 +1 0.0356 C 2.11521470 +1 -4.95434375 +1 1.54982554 +1 -0.0269 C 5.63720513 +1 1.63781098 +1 0.08515768 +1 0.2842 C 5.77671629 +1 1.09375761 +1 -1.35351623 +1 0.0646 C 4.84403990 +1 -0.11533336 +1 -1.52863588 +1 0.0835 C 5.22242832 +1 -1.14398525 +1 -0.44359304 +1 0.0295 C 5.08204012 +1 -0.52849001 +1 0.95966880 +1 0.0316 C 5.65736497 +1 -1.45551210 +1 2.03903597 +1 -0.0310 C 2.11545472 +1 5.21707998 +1 1.56283225 +1 0.2885 C 3.13719189 +1 5.51000130 +1 0.43531286 +1 0.0450 C 3.53410278 +1 4.18301195 +1 -0.22190511 +1 0.0716 C 4.08921016 +1 3.25859897 +1 0.87965398 +1 0.0218 C 3.02838497 +1 3.04195422 +1 1.97016340 +1 0.0351 C 3.57291814 +1 2.29281989 +1 3.20234176 +1 -0.0076 C -2.99182222 +1 5.30366269 +1 0.45083259 +1 0.2916 C -2.06654569 +1 5.76455218 +1 -0.69994504 +1 0.0605 C -0.69573787 +1 5.08165024 +1 -0.56249169 +1 0.0831 C -0.15172498 +1 5.38240578 +1 0.84887265 +1 0.0323 C -1.15690241 +1 4.92420127 +1 1.92230152 +1 0.0344 C -0.74315404 +1 5.38713813 +1 3.32342050 +1 -0.0252 O -6.27680753 +1 1.24698988 +1 -2.06073221 +1 -0.5727 O -4.83080571 +1 3.73498868 +1 -1.93755367 +1 -0.5898 O -3.10086409 +1 3.90671099 +1 0.31864329 +1 -0.4357 O -5.62547707 +1 1.59824791 +1 1.48393270 +1 -0.4661 O -3.61318208 +1 1.91050129 +1 3.75421497 +1 -0.5551 O -5.31011038 +1 -4.08324522 +1 -2.30804895 +1 -0.5638 O -6.38510120 +1 -1.44539791 +1 -1.94692326 +1 -0.5928 O -4.94769014 +1 0.07410023 +1 -0.03780326 +1 -0.4438 O -4.39335147 +1 -3.31294001 +1 1.09857495 +1 -0.4191 H -3.11284098 +1 -0.91072026 +1 2.67537399 +1 0.1223 O -5.13024664 +1 -0.65649001 +1 2.88793970 +1 -0.5898 O 0.19059229 +1 -5.27395731 +1 -3.77667695 +1 -0.5791 O -2.52102602 +1 -4.37060870 +1 -3.45721976 +1 -0.5826 O -3.15352606 +1 -3.76206581 +1 -0.74954245 +1 -0.4484 O -0.55880332 +1 -6.28346828 +1 -0.39486064 +1 -0.4583 O -3.02655553 +1 -6.87147211 +1 0.87919692 +1 -0.5470 O 5.15651966 +1 -3.30908540 +1 -2.83403623 +1 -0.5644 O 2.82158213 +1 -4.87941670 +1 -3.34750099 +1 -0.5949 O 0.91449460 +1 -4.75872223 +1 -1.22399692 +1 -0.4369 O 4.03460648 +1 -4.15896560 +1 0.49561701 +1 -0.4386 O 1.96138603 +1 -4.08431320 +1 2.64998463 +1 -0.5396 O 5.43187484 +1 2.16983302 +1 -2.19981330 +1 -0.5733 O 5.08708025 +1 -0.61874556 +1 -2.81522528 +1 -0.5949 O 4.24846175 +1 -2.16110829 +1 -0.56355658 +1 -0.4474 O 5.89704835 +1 0.64015659 +1 1.05099852 +1 -0.4675 O 6.93672854 +1 -1.91221628 +1 1.66194943 +1 -0.5401 O 2.48729944 +1 6.34924191 +1 -0.50048218 +1 -0.5641 O 4.54886488 +1 4.48914811 +1 -1.14463909 +1 -0.5949 O 4.29392107 +1 2.01162966 +1 0.23680058 +1 -0.4401 O 2.66145697 +1 4.32109537 +1 2.48933873 +1 -0.4127 O 4.95715032 +1 2.07434097 +1 3.14601208 +1 -0.5771 O -2.71515342 +1 5.39995114 +1 -1.90067286 +1 -0.5796 O 0.11642735 +1 5.64939670 +1 -1.55702764 +1 -0.6030 O 1.00387096 +1 4.57704331 +1 0.96337101 +1 -0.4531 O -2.40143795 +1 5.58318991 +1 1.69272342 +1 -0.4568 O -0.39657446 +1 6.75490183 +1 3.31354465 +1 -0.5475 H -6.95851375 +1 0.51158901 +1 0.48123318 +1 0.1588 H -6.87285049 +1 2.71059519 +1 -0.78626132 +1 0.1614 H -3.84049125 +1 2.06539923 +1 -1.27401200 +1 0.1566 H -5.16376728 +1 4.15339383 +1 0.65250677 +1 0.1489 H -3.55062496 +1 1.54436303 +1 1.28855858 +1 0.1661 H -5.24925155 +1 3.09371551 +1 3.33389767 +1 0.1368 H -3.59202469 +1 3.72545922 +1 2.95003808 +1 0.1664 H -4.56205918 +1 -5.06129106 +1 0.17028242 +1 0.1714 H -6.50857643 +1 -3.67206762 +1 -0.69642393 +1 0.1539 H -4.35186306 +1 -1.68051711 +1 -1.78995189 +1 0.1540 H -6.24057567 +1 -1.41750676 +1 0.70495925 +1 0.1620 H -3.14013708 +1 -1.76593647 +1 0.50318848 +1 0.1546 H 0.87770592 +1 -6.83618055 +1 -1.65240695 +1 0.1500 H -1.22594428 +1 -6.54639295 +1 -3.07013754 +1 0.1572 H -1.13257580 +1 -3.52468866 +1 -2.23367836 +1 0.1625 H -3.10039448 +1 -5.77684285 +1 -1.30022957 +1 0.1617 H -0.83535364 +1 -4.35072580 +1 0.33358528 +1 0.1613 H -2.77054533 +1 -5.11700636 +1 1.78792464 +1 0.1698 H -1.39282521 +1 -6.27579082 +1 1.98642863 +1 0.1331 H 5.80519163 +1 -3.54235242 +1 -0.14775418 +1 0.1680 H 4.94659827 +1 -5.13795910 +1 -1.94950322 +1 0.1548 H 2.56164590 +1 -3.13239404 +1 -2.29945397 +1 0.1584 H 2.61779440 +1 -5.96209424 +1 -0.95588597 +1 0.1475 H 2.23086303 +1 -3.13019134 +1 0.33138672 +1 0.1674 H 2.80151687 +1 -5.77511291 +1 1.82906402 +1 0.1356 H 1.09388664 +1 -5.35393895 +1 1.38578909 +1 0.1629 H 6.37073715 +1 2.43448228 +1 0.33816740 +1 0.1594 H 6.83440712 +1 0.83666943 +1 -1.59519327 +1 0.1602 H 3.76716041 +1 0.16694204 +1 -1.48651645 +1 0.1612 H 6.25190047 +1 -1.53633913 +1 -0.61701369 +1 0.1640 H 4.02504833 +1 -0.25276398 +1 1.17185413 +1 0.1547 H 5.06288554 +1 -2.38729546 +1 2.12470733 +1 0.1593 H 5.71938438 +1 -0.95193645 +1 3.02164858 +1 0.1392 H 1.83963855 +1 6.10084326 +1 2.18005406 +1 0.1699 H 4.02130219 +1 6.06448525 +1 0.82405416 +1 0.1559 H 2.68326770 +1 3.71535330 +1 -0.76895008 +1 0.1579 H 5.02879631 +1 3.66934173 +1 1.31610125 +1 0.1661 H 2.11994409 +1 2.54802326 +1 1.56023137 +1 0.1539 H 3.05392845 +1 1.32945802 +1 3.34529791 +1 0.1172 H 3.45648404 +1 2.91427450 +1 4.11763681 +1 0.1640 H -3.96373289 +1 5.83634923 +1 0.49105339 +1 0.1490 H -1.96958222 +1 6.87487999 +1 -0.72002134 +1 0.1565 H -0.74330045 +1 3.98842003 +1 -0.77023887 +1 0.1607 H 0.09131759 +1 6.46577886 +1 0.95216874 +1 0.1628 H -1.30958061 +1 3.82119183 +1 1.89074866 +1 0.1630 H 0.18800059 +1 4.88221226 +1 3.65407327 +1 0.1661 H -1.54633118 +1 5.21543396 +1 4.06263065 +1 0.1344 H -5.85997550 +1 1.68300088 +1 -2.84198997 +1 0.3605 H -4.04314000 +1 4.33902858 +1 -1.94135781 +1 0.3706 H -4.12956637 +1 1.07197957 +1 3.81043977 +1 0.3367 H -5.86494359 +1 -3.62435514 +1 -2.98509411 +1 0.3480 H -6.34564314 +1 -0.46084811 +1 -2.02604817 +1 0.3664 H -5.25912741 +1 0.13088446 +1 2.32497607 +1 0.3436 H -0.27643282 +1 -4.67483147 +1 -4.40704060 +1 0.3615 H -3.43442506 +1 -4.14258181 +1 -3.14226432 +1 0.3656 H -2.54143786 +1 -7.58773321 +1 0.41635558 +1 0.3241 H 4.82934075 +1 -3.55117814 +1 -3.73811246 +1 0.3565 H 1.85790708 +1 -5.01945146 +1 -3.53151951 +1 0.3702 H 2.80383635 +1 -3.61196963 +1 2.81641933 +1 0.3182 H 5.00700257 +1 1.82905798 +1 -3.02331078 +1 0.3621 H 5.04623278 +1 -1.61013836 +1 -2.81827677 +1 0.3697 H 7.54815361 +1 -1.14811845 +1 1.57027975 +1 0.3266 H 3.05873206 +1 6.41437846 +1 -1.30887369 +1 0.3548 H 4.88564679 +1 3.65895119 +1 -1.56438317 +1 0.3675 H 5.21605312 +1 1.47541811 +1 2.42076076 +1 0.3403 H -2.04409488 +1 5.26725424 +1 -2.61391131 +1 0.3620 H 1.02774349 +1 5.82854533 +1 -1.20515876 +1 0.3697 H -1.16802923 +1 7.29121055 +1 3.03089853 +1 0.3240 H -4.12417712 +1 -2.33330290 +1 3.15893797 +1 0.1667 ------------- 用pdb格式打开在pymol中没有看到东西 输入文件的坐标部分如下： --------------------------------- C -5.9639 1 0.9384 1 0.7057 1 C -6.3291 1 2.1268 1 -0.1809 1 C -5.0908 1 2.9921 1 -0.4484 1 C -4.4389 1 3.3723 1 0.8849 1 C -4.1029 1 2.1198 1 1.6916 1 C -3.6529 1 2.4977 1 3.1091 1 C -4.4740 1 -3.9586 1 -0.7511 1 C -5.3109 1 -3.2034 1 -1.7203 1 C -5.1663 1 -1.6882 1 -1.5447 1 C -5.3618 1 -1.3142 1 -0.1363 1 C -4.3964 1 -2.0976 1 0.7521 1 C -4.4479 1 -1.8287 1 2.2574 1 C 0.3020 1 -6.0789 1 -1.5113 1 C -0.4767 1 -5.8116 1 -2.7819 1 C -1.4334 1 -4.6415 1 -2.5315 1 C -2.3083 1 -4.9829 1 -1.3525 1 C -1.4897 1 -5.3318 1 -0.1006 1 C -2.3119 1 -5.8761 1 1.0004 1 C 4.8522 1 -3.6778 1 -0.1914 1 C 4.7610 1 -4.4342 1 -1.5350 1 C 3.3001 1 -4.4900 1 -1.9529 1 C 2.4714 1 -5.1141 1 -0.8556 1 C 2.7018 1 -4.3930 1 0.4708 1 C 2.0445 1 -5.1770 1 1.6475 1 C 5.6105 1 1.5719 1 0.1995 1 C 6.0421 1 0.8697 1 -1.0895 1 C 5.1829 1 -0.3476 1 -1.3576 1 C 5.2367 1 -1.2730 1 -0.1655 1 C 4.7924 1 -0.5069 1 1.0688 1 C 4.8700 1 -1.3373 1 2.3720 1 C 2.1938 1 5.6076 1 0.6789 1 C 3.0961 1 5.5437 1 -0.5583 1 C 3.4311 1 4.0931 1 -0.8745 1 C 4.0699 1 3.4537 1 0.3390 1 C 3.1224 1 3.5547 1 1.5396 1 C 3.7161 1 3.0358 1 2.8376 1 C -3.0848 1 5.3784 1 0.9904 1 C -2.4929 1 6.1950 1 -0.1661 1 C -1.0942 1 5.6825 1 -0.5162 1 C -0.2296 1 5.6859 1 0.7297 1 C -0.8808 1 4.9511 1 1.8986 1 C -0.1631 1 5.1840 1 3.2193 1 O -6.8913 1 1.6523 1 -1.4049 1 O -5.4813 1 4.1957 1 -1.1165 1 O -3.2147 1 4.0435 1 0.5326 1 O -5.3524 1 1.3818 1 1.8967 1 O -3.2236 1 1.3339 1 3.7646 1 O -4.9377 1 -3.5938 1 -3.0571 1 O -6.1304 1 -1.0220 1 -2.4119 1 O -5.0706 1 0.1041 1 -0.0295 1 O -4.7521 1 -3.4962 1 0.5244 1 H -3.9716 1 -0.8486 1 2.4739 1 O -5.5369 1 -1.9009 1 3.0181 1 O 0.4052 1 -5.5217 1 -3.8747 1 O -2.2729 1 -4.4323 1 -3.6759 1 O -3.0931 1 -3.7815 1 -1.0983 1 O -0.5553 1 -6.3867 1 -0.4471 1 O -3.0218 1 -6.9560 1 0.5683 1 O 5.5336 1 -3.7723 1 -2.5332 1 O 3.1577 1 -5.2424 1 -3.1698 1 O 1.0876 1 -4.9323 1 -1.2331 1 O 4.0868 1 -4.3337 1 0.7712 1 O 2.1727 1 -4.4536 1 2.8453 1 O 5.9820 1 1.8142 1 -2.1841 1 O 5.6516 1 -1.0047 1 -2.5355 1 O 4.3626 1 -2.3557 1 -0.4114 1 O 5.6298 1 0.6450 1 1.2814 1 O 6.1059 1 -1.9553 1 2.5530 1 O 2.3812 1 6.1854 1 -1.6476 1 O 4.3464 1 4.0571 1 -1.9881 1 O 4.2957 1 2.0750 1 0.0131 1 O 2.8468 1 4.9630 1 1.7686 1 O 4.9277 1 3.6866 1 3.1963 1 O -3.3550 1 6.1204 1 -1.3189 1 O -0.4981 1 6.5272 1 -1.5195 1 O 0.9632 1 4.9903 1 0.3843 1 O -2.2398 1 5.4637 1 2.1134 1 O -0.1423 1 6.5816 1 3.5141 1 H -6.8884 1 0.4026 1 1.0026 1 H -7.1051 1 2.7399 1 0.3254 1 H -4.3652 1 2.4177 1 -1.0631 1 H -5.1369 1 4.0104 1 1.4680 1 H -3.2887 1 1.5607 1 1.1828 1 H -4.5228 1 2.8843 1 3.6819 1 H -2.7731 1 3.1734 1 3.0492 1 H -4.7621 1 -5.0293 1 -0.7718 1 H -6.3764 1 -3.4898 1 -1.5892 1 H -4.1523 1 -1.3740 1 -1.8724 1 H -6.4069 1 -1.5420 1 0.1641 1 H -3.3544 1 -1.9217 1 0.4093 1 H 0.9562 1 -6.9621 1 -1.6592 1 H -1.0628 1 -6.7158 1 -3.0525 1 H -0.8456 1 -3.7270 1 -2.3021 1 H -2.9636 1 -5.8406 1 -1.6156 1 H -0.9526 1 -4.4259 1 0.2532 1 H -3.0538 1 -5.1130 1 1.3192 1 H -1.6471 1 -6.2361 1 1.8145 1 H 5.9006 1 -3.6941 1 0.1698 1 H 5.1467 1 -5.4677 1 -1.4035 1 H 2.9336 1 -3.4601 1 -2.1515 1 H 2.7493 1 -6.1842 1 -0.7468 1 H 2.2643 1 -3.3731 1 0.4172 1 H 2.5813 1 -6.1383 1 1.7961 1 H 0.9557 1 -5.2864 1 1.4556 1 H 6.3423 1 2.3672 1 0.4481 1 H 7.1051 1 0.5588 1 -1.0021 1 H 4.1329 1 -0.0274 1 -1.5290 1 H 6.2790 1 -1.6302 1 -0.0225 1 H 3.7521 1 -0.1447 1 0.9235 1 H 4.1099 1 -2.1471 1 2.3397 1 H 4.7164 1 -0.6685 1 3.2458 1 H 2.0495 1 6.6665 1 0.9751 1 H 4.0346 1 6.1042 1 -0.3598 1 H 2.4986 1 3.5467 1 -1.1314 1 H 5.0208 1 3.9778 1 0.5745 1 H 2.1843 1 3.0029 1 1.3165 1 H 3.9537 1 1.9559 1 2.7292 1 H 3.0000 1 3.2137 1 3.6682 1 H -4.1095 1 5.7409 1 1.2105 1 H -2.4306 1 7.2637 1 0.1310 1 H -1.1689 1 4.6466 1 -0.9105 1 H -0.0148 1 6.7346 1 1.0268 1 H -0.9080 1 3.8620 1 1.6806 1 H 0.8960 1 4.8617 1 3.1258 1 H -0.7299 1 4.6932 1 4.0391 1 H -7.1024 1 2.4110 1 -1.9216 1 H -4.6961 1 4.6956 1 -1.2613 1 H -2.9533 1 1.5908 1 4.6297 1 H -5.4818 1 -3.1017 1 -3.6481 1 H -6.0194 1 -0.0954 1 -2.2838 1 H -5.2638 1 -1.6795 1 3.9243 1 H -0.1362 1 -5.3659 1 -4.6297 1 H -2.8384 1 -3.7070 1 -3.4718 1 H -3.5259 1 -7.2637 1 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3楼2014-01-09 08:45:38
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4楼2014-01-09 08:46:48