{"id":1487,"date":"2024-05-13T09:06:04","date_gmt":"2024-05-13T01:06:04","guid":{"rendered":"https:\/\/www.homechemer.com\/?p=1487"},"modified":"2024-05-13T22:24:39","modified_gmt":"2024-05-13T14:24:39","slug":"amb2gjf-py-%e9%9d%99%e7%94%b5%e5%b5%8c%e5%85%a5%e7%9a%84qm-mm%e6%96%b9%e6%b3%95","status":"publish","type":"post","link":"https:\/\/www.homechemer.com\/computchem\/13","title":{"rendered":"amb2gjf.py: \u9759\u7535\u5d4c\u5165\u7684QM\/MM\u65b9\u6cd5"},"content":{"rendered":"\n

amb2gjf.py: \u9759\u7535\u5d4c\u5165\u7684QM\/MM\u65b9\u6cd5
amb2gjf.py: QM\/MM Method with Electrostatic Embedding Scheme<\/strong><\/p>\n\n\n\n

Jiawei Xu, Yingqi Li
Released: 2024-05-13 \/ Updated: 2024-05-13<\/p>\n\n\n\n

\u9759\u7535\u5d4c\u5165(electrostatic embedding, EE)\u7684QM\/MM\u65b9\u6cd5\u662f\u76ee\u524d\u666e\u904d\u4f7f\u7528\u7684\u4e00\u79cd\u5d4c\u5165\u65b9\u6cd5\uff0c\u5373\u5728\u8ba1\u7b97QM\u533a\u65f6MM\u533a\u4ee5\u80cc\u666f\u7535\u8377\u5f62\u5f0f\u5448\u73b0\uff0c\u540c\u65f6\u5bf9QM\/MM\u8fde\u63a5\u5904\u7684\u80cc\u666f\u7535\u8377\u548c\u8fde\u63a5\u539f\u5b50(linker atom)\u505a\u7279\u6b8a\u5904\u7406\u3002\u672c\u6587\u7b80\u5355\u56de\u987e\u9759\u7535\u5d4c\u5165\u65b9\u6cd5\u5904\u7406\u8fb9\u754c\u60c5\u51b5\u7684\u57fa\u672c\u539f\u7406\uff0c\u5e76\u4ecb\u7ecd\u57fa\u4e8eAMBER\u683c\u5f0f\u7684\u53c2\u6570\uff0c\u751f\u6210Gaussian\u8f93\u5165\u6587\u4ef6\uff0c\u5e76\u6309\u9759\u7535\u5d4c\u5165\u65b9\u6cd5\u6dfb\u52a0\u80cc\u666f\u7535\u8377\u8bbe\u7f6e\u7684\u811a\u672camb2gjf.py\u3002<\/p>\n\n\n\n

1. \u9759\u7535\u5d4c\u5165\u65b9\u6cd5\u5bf9\u8fb9\u754c\u7684\u5904\u7406
1.1 \u8fde\u63a5\u539f\u5b50
<\/strong>\u672c\u6587\u4ec5\u8ba8\u8bba\u4f7f\u7528\u6c22\u539f\u5b50\u4f5c\u4e3a\u8fde\u63a5\u539f\u5b50\u7684\u60c5\u51b5\u3002
\u5f53QM\/MM\u8fb9\u754c\u901a\u8fc7\u5316\u5b66\u952e\u76f8\u8fde\u65f6\uff0c\u5207\u65ad\u8fb9\u754c\u5bfc\u81f4QM\u548cMM\u533a\u7684\u8fb9\u754c\u539f\u5b50\u6210\u952e\u4e0d\u9971\u548c\uff0c\u9700\u8981\u6dfb\u52a0\u8fde\u63a5\u539f\u5b50\u4fdd\u6301\u7ed3\u6784\u7684\u5b8c\u6574\u6027\u3002\u5207\u65ad\u5316\u5b66\u952e\u3001\u8865\u5168\u8fde\u63a5\u539f\u5b50\u7684\u76ee\u7684\u662f\u4e3a\u4e86\u5c3d\u53ef\u80fd\u51cf\u5c11\u5206\u5c42\u8bbe\u7f6e\u5bf9QM\u548cMM\u533a\u4ea7\u751f\u7684\u5f71\u54cd\uff0c\u5c24\u5176\u662f\u4e0d\u80fd\u5bf9QM\u533a\u7684\u7535\u5b50\u7ed3\u6784\u4ea7\u751f\u663e\u8457\u5b9a\u91cf\u5f71\u54cd\u6216\u5b9a\u6027\u5f71\u54cd\u3002\u56e0\u6b64\uff0c\u5e38\u89c4\u7684\u505a\u6cd5\u662f\u5207\u65ad\u5171\u4ef7\u6210\u5206\u9ad8\u3001\u6781\u6027\u4f4e\u7684\u5316\u5b66\u952e\uff0c\u5e76\u7528\u6c22\u539f\u5b50\u4f5c\u4e3a\u8fde\u63a5\u539f\u5b50\uff08\u5982\u56fe1<\/strong>\u6240\u793a\uff09\u3002\u5728\u751f\u7269\u4f53\u7cfb\u7684\u7814\u7a76\u4e2d\uff0c\u4e00\u822c\u662f\u5207\u65ad\u6c28\u57fa\u9178\u7684alpha-C\u548cbeta-C\u4e4b\u95f4\u7684\u78b3\u78b3\u5355\u952e\uff0c\u5bf9\u4e8e\u6d89\u53ca\u6838\u9178\u7684\u60c5\u51b5\uff0c\u82e5\u6709\u5fc5\u8981\u5c06\u78f7\u9178\u57fa\u56e2\u4fdd\u7559\u5728QM\u533a\u57df\uff0c\u4e5f\u6709\u53ef\u80fd\u5207\u65ad3′,5′-\u78f7\u9178\u4e8c\u916f\u7ed3\u6784\u4e2d\u7684C-O\u5355\u952e\uff0c\u5e76\u8865\u5168\u4e3a-OH\u3002
\u8fde\u63a5\u539f\u5b50\u7684\u4f4d\u7f6e\u53d6\u51b3\u4e8e\u88ab\u5207\u65ad\u7684\u5316\u5b66\u952e\u3002\u8003\u8651\u88ab\u5207\u65ad\u7684\u5316\u5b66\u952e\u7684\u6210\u952e\u539f\u5b50\u4e3aQM\u533a\u7684A\u539f\u5b50\u548cMM\u533a\u7684B\u539f\u5b50\uff0c\u5176\u5171\u4ef7\u534a\u5f84\u5206\u522b\u4e3ar_{\\text{A}}<\/span>\u548cr_{\\text{B}}<\/span>\uff0c\u8fde\u63a5\u539f\u5b50\u7684\u5171\u4ef7\u534a\u5f84\u4e3ar_{\\text{L}}<\/span>\uff08\u4e00\u822c\u4f7f\u7528\u6c22\u539f\u5b50\uff09\uff0c\u5219A-L\u952e\u952e\u957fR<\/span>\u4e3a\uff1a<\/p>\n\n\n\n

$$ R = g \\cdot r \\tag{1} $$<\/p>\n\n\n\n

\u5176\u4e2dr<\/span>\u4e3a\u539fA-B\u952e\u957f\uff0c\u6bd4\u4f8b\u7cfb\u6570g<\/span>\uff1a<\/p>\n\n\n\n

$$ g = \\frac{r_{\\text{A}} + r_{\\text{L}}}{r_{\\text{A}} + r_{\\text{B}}} \\tag{2} $$<\/p>\n\n\n\n

1.2 \u80cc\u666f\u7535\u8377\u5904\u7406<\/strong>
\u6211\u4eec\u5c06\u622a\u65ad\u7684\u5316\u5b66\u952e\u79f0\u4f5cQM\/MM\u952e\uff0c\u5982\u56fe1<\/strong>\uff0cQM\u533a\u57df\u7684\u539f\u5b50\u79f0\u4e3aQM\u539f\u5b50\uff0c\u4e0eQM\u539f\u5b50\u76f4\u63a5\u76f8\u8fde\u7684MM\u533a\u539f\u5b50\u4e3aMM1\u539f\u5b50\uff0c\u4e0eMM1\u539f\u5b50\u76f4\u63a5\u76f8\u8fde\u7684MM\u533a\u539f\u5b50\u4e3aMM2\u539f\u5b50\uff0c\u4ee5\u6b64\u7c7b\u63a8\u3002\u7531\u4e8eQM\/MM\u952e\u88ab\u622a\u65ad\uff0cQM\u539f\u5b50\u4f7f\u7528\u8fde\u63a5\u539f\u5b50L\u5c01\u7aef\uff0c\u6545\u800cMM\u539f\u5b50\u7684\u7535\u8377\u901a\u5e38\u9700\u8981\u8fdb\u884c\u7279\u6b8a\u5904\u7406\uff0c\u4ee5\u786e\u4fdd\u5176\u5bf9\u6a21\u62df\u7ed3\u679c\u7684\u4e0d\u5229\u5f71\u54cd\u5c3d\u53ef\u80fd\u5c0f\u3002<\/p>\n\n\n

\n
\"\"<\/figure>\n<\/div>\n\n\n

\u56fe1.<\/strong> QM\/MM\u8fb9\u754c\u4e0a\u7684\u539f\u5b50\u5206\u7c7b\u3002<\/p>\n\n\n\n

1.2.1 \u4e0d\u5904\u7406\u80cc\u666f\u7535\u8377<\/strong>
\u4fdd\u7559\u5168\u90e8MM\u533a\u57df\u7684\u539f\u5b50\u7535\u8377\u4f5c\u4e3a\u80cc\u666f\u7535\u8377\u52a0\u5165QM\u8ba1\u7b97\u3002\u6b64\u65f6\uff0c\u7531\u4e8eQM\/MM\u952e\u622a\u65ad\u540e\u4f7f\u7528L\u5c01\u7aef\uff0cL\u4e0eMM1\u7684\u8ddd\u79bb\u5f80\u5f80\u8fc7\u8fd1\uff0c\u5bfc\u81f4L\u53d7\u5230\u4e0d\u5408\u7406\u7684\u9759\u7535\u4f5c\u7528\u3002\u8003\u8651\u5230\u8fd9\u4e00\u70b9\uff0c\u6709\u5fc5\u8981\u5bf9\u80cc\u666f\u7535\u8377\u8fdb\u884c\u5904\u7406\uff0c\u624d\u80fd\u8f83\u4e3a\u51c6\u786e\u5730\u5728QM\u8ba1\u7b97\u4e2d\u91cd\u73b0\u8fb9\u754c\u9644\u8fd1\u7684\u7535\u5b50\u7ed3\u6784\u3002
1.2.2 Zn<\/em>\u65b9\u6cd5<\/strong>
\u65e2\u7136MM\u539f\u5b50\u7535\u8377\u4e0eL\u8fc7\u8fd1\u4f1a\u4ea7\u751f\u4e0d\u5408\u7406\u9759\u7535\u4f5c\u7528\uff0c\u90a3\u4e48\u5c31\u76f4\u63a5\u5ffd\u7565n<\/em>\u5c42MM\u539f\u5b50\u7684\u7535\u8377\u3002\u5982\u56fe2<\/strong>\u6240\u793a\uff0cZ1\u65b9\u6cd5\u8868\u793a\u5ffd\u7565\u6240\u6709MM1\u539f\u5b50\u7684\u7535\u8377\uff08\u7528\u7070\u8272\u8868\u793a\uff09\uff0cZ2\u65b9\u6cd5\u5ffd\u7565\u6240\u6709MM1\u3001MM2\u539f\u5b50\u7684\u7535\u8377\uff0c\u4ee5\u6b64\u7c7b\u63a8\u3002\u8be5\u65b9\u6cd5\u80fd\u591f\u907f\u514d\u4e0d\u5408\u7406\u7684\u9759\u7535\u4f5c\u7528\uff0c\u4f46\u4f1a\u5bfc\u81f4\u6574\u4e2a\u4f53\u7cfb\u7684\u7535\u8377\u4e0d\u5b88\u6052\uff0c\u4e14\u5c40\u90e8\u9759\u7535\u52bf\u3001\u5076\u6781\u77e9\u60c5\u51b5\u4e0e\u5b9e\u9645\u4e0d\u7b26\u3002\u7531\u4e8e\u5ffd\u7565\u66f4\u591a\u5c42\u7535\u8377\u5e76\u6ca1\u6709\u5f88\u660e\u786e\u7684\u7269\u7406\u610f\u4e49\uff0cZ2\u548cZ3\u65b9\u6cd5\u4f7f\u7528\u5e76\u4e0d\u5982Z1\u65b9\u6cd5\u4f7f\u7528\u5e7f\u6cdb\u3002<\/p>\n\n\n

\n
\"\"<\/figure>\n<\/div>\n\n\n

\u56fe2. a).<\/strong> Z1\u65b9\u6cd5\uff1bb).<\/strong> Z2\u65b9\u6cd5\u548cc).<\/strong> Z3\u65b9\u6cd5\u5bf9\u8fb9\u754c\u9644\u8fd1\u7535\u8377\u7684\u5904\u7406\u3002<\/p>\n\n\n\n

1.2.3 \u91cd\u7ec4\u7535\u8377\u548c\u5076\u6781\u77e9(redistributed charge and dipole, RCD)<\/strong>
\u4e3a\u4e86\u907f\u514dZn<\/em>\u65b9\u6cd5\u7684\u7f3a\u9677\uff0cRCD\u65b9\u6cd5\u5c06MM1\u539f\u5b50\u7684\u7535\u8377\u6cbfMM1-MM2\u952e\u8f74\u5411MM2\u539f\u5b50\u65b9\u5411\u79fb\u52a8\uff0c\u4f7f\u4e4b\u9002\u5f53\u5730\u8fdc\u79bbL\u539f\u5b50\u3002\u8003\u8651MM1\u539f\u5b50\u7535\u8377\u4e3aq<\/span>\uff0c\u4e0e\u4e4b\u76f4\u63a5\u76f8\u8fde\u7684MM2\u539f\u5b50\u4e2a\u6570\u4e3an<\/span>\u7684\u60c5\u51b5\uff0c\u5047\u8bbe\u79fb\u52a8\u540e\u7684\u7535\u8377\u4e3aq'<\/span>\u3002\u4e3a\u4e86\u91cd\u73b0MM1-MM2\u952e\u4e0a\u7684\u5076\u6781\u77e9\uff0cMM2\u539f\u5b50\u7684\u7535\u8377\u4e5f\u9700\u8981\u9002\u5f53\u8c03\u6574\uff0c\u5047\u8bbe\u5176\u53d8\u5316\u91cf\u4e3a\\Delta q<\/span>\uff0c\u6839\u636e\u7535\u8377\u5b88\u6052\uff1a<\/p>\n\n\n\n

$$ nq’ + n\\Delta q = q \\tag{3} $$<\/p>\n\n\n\n

\u8c03\u6574\u7535\u8377\u524d\u540e\u7684\u5076\u6781\u77e9\u76f8\u7b49\uff1a<\/p>\n\n\n\n

$$ \\frac{q}{n} \\cdot R_{\\text{MM1-MM2}} = q’R_{q’-\\text{MM2}} \\tag{4} $$<\/p>\n\n\n\n

\u5176\u4e2dR_{\\text{MM1-MM2}}<\/span>\u4e3aMM1-MM2\u952e\u957f\uff0cR_{q'-\\text{MM2}}<\/span>\u4e3a\u79fb\u52a8\u540e\u70b9\u7535\u8377\u4e0e\u76f8\u5e94MM2\u539f\u5b50\u4e4b\u95f4\u7684\u8ddd\u79bb\u3002\u4e0a\u8ff0\u4e24\u5f0f\u7684\u89e3\u4e0d\u552f\u4e00\uff0c\u4e00\u822c\u9009MM1-MM2\u952e\u8f74\u4e2d\u70b9\u4f5c\u4e3a\u79fb\u52a8\u540e\u80cc\u666f\u7535\u8377\u7684\u4f4d\u7f6e\uff0c\u5373\uff1a<\/p>\n\n\n\n

$$R_{q’-\\text{MM2}} = \\frac{1}{2} R_{\\text{MM1-MM2}} \\tag{5} $$<\/p>\n\n\n\n

\u5219\u53ef\u5f97\uff1a<\/p>\n\n\n\n

$$q’ = 2\\times \\frac{q}{n} \\tag{6} $$<\/p>\n\n\n\n

$$\\Delta q = – \\frac{q}{n} \\tag{7} $$<\/p>\n\n\n

\n
\"\"<\/figure>\n<\/div>\n\n\n

\u56fe3. a).<\/strong> RCD\u65b9\u6cd5\u548cb).<\/strong> CS\u65b9\u6cd5\u5bf9\u8fb9\u754c\u9644\u8fd1\u7535\u8377\u7684\u5904\u7406\u3002\u9ec4\u8272\u5706\u5708\u8868\u793a\u7535\u8377\u53d1\u751f\u4e86\u53d8\u5316\u3002<\/p>\n\n\n\n

1.2.4 \u7535\u8377\u79fb\u52a8(charge shifting, CS)<\/strong>
CS\u65b9\u6cd5\u4e0eRCD\u65b9\u6cd5\u7c7b\u4f3c\uff0c\u4f46\u91c7\u7528\u4e0d\u540c\u7684\u5206\u914d\u7b56\u7565\u3002RCD\u65b9\u6cd5\u91c7\u7528\u201c\u6dfb\u52a0-\u6263\u9664\u201d\u7b56\u7565\uff0c\u5373\u5148\u5728MM1-MM2\u539f\u5b50\u4e4b\u95f4\u6dfb\u52a0\u80cc\u666f\u7535\u8377\uff0c\u7136\u540e\u4eceMM2\u539f\u5b50\u7535\u8377\u4e2d\u6263\u9664\u76f8\u5e94\u7684\u90e8\u5206\uff0c\u4ee5\u5f25\u8865\u65b0\u589e\u7684\u7535\u8377\uff0c\u5e76\u91cd\u73b0\u5c40\u90e8\u7684\u5076\u6781\u77e9\u3002CS\u65b9\u6cd5\u5219\u91c7\u7528\u201c\u6263\u9664-\u6dfb\u52a0\u201d\u7b56\u7565\uff0c\u76f4\u63a5\u5c06MM1\u539f\u5b50\u7535\u8377\u52a0\u5230\u4e0e\u4e4b\u76f8\u8fde\u7684MM2\u539f\u5b50\u4e0a\uff0c\u7531\u4e8eMM1\u548cMM2\u539f\u5b50\u4e00\u822c\u662f\u5e26\u76f8\u53cd\u7535\u8377\u7684\uff0c\u56e0\u6b64\u5b9e\u9645\u4e0a\u4f7f\u5f97MM2\u539f\u5b50\u7684\u51c0\u7535\u8377\u91cf\u51cf\u5c11\uff0c\u662f\u4e00\u79cd\u6263\u9664\uff0c\u8be5\u8fc7\u7a0b\u662f\u7535\u8377\u5b88\u6052\u7684\u3002\u4e3a\u4e86\u91cd\u73b0\u5076\u6781\u77e9\uff0c\u6cbf\u7740MM1-MM2\u952e\u8f74\u65b9\u5411\uff0c\u5728MM2\u539f\u5b50\u524d\u540e\u5404\u6dfb\u52a0\u4e00\u5bf9\u7535\u8377\u91cf\u76f8\u7b49\u3001\u7b26\u53f7\u76f8\u53cd\u7684\u80cc\u666f\u7535\u8377+\\delta q<\/span>\u548c-\\delta q<\/span>\uff0c\u5176\u5230MM2\u539f\u5b50\u7684\u8ddd\u79bb\u4e3a\\delta r<\/span>\uff0c\u5219\uff1a<\/p>\n\n\n\n

$$ \\delta r \\delta q = \\frac{q}{n} \\cdot R_{\\text{MM1-MM2}} \\tag{8} $$<\/p>\n\n\n\n

\u663e\u7136\uff0c\\delta q<\/span>\u7684\u5177\u4f53\u6570\u503c\u4e5f\u662f\u4f9d\u8d56\u4e8e\u8ddd\u79bb\\delta r<\/span>\u7684\u3002\u4e0d\u540c\u7684\u7a0b\u5e8f\u4e2d\u5bf9\u8be5\u8ddd\u79bb\u6709\u4e0d\u540c\u7684\u4ea7\u751f\u65b9\u6cd5\uff0c\u6ca1\u6709\u660e\u663e\u5dee\u5f02\uff0c\u4e00\u822c\u6765\u8bf4\u4f1a\u4f7f\\delta q<\/span>\u66f4\u9760\u8fd1MM2\u539f\u5b50\u3002<\/p>\n\n\n\n

2. \u4f7f\u7528\u65b9\u6cd5<\/strong>
\u67e5\u770b\u5e2e\u52a9\uff1apython amb2gjf.py -h\uff1b\u5bf9\u4e8e\u96c6\u7fa4\u7528\u6237\uff0c\u5b9e\u9645\u4e0a\u53ef\u4ee5\u53bb\u6389\u540e\u7f00\u653e\u5728\u4e00\u4e2a\u6dfb\u52a0\u8fc7\u73af\u5883\u53d8\u91cf\u7684\u8def\u5f84\u91cc\uff0c\u6ce8\u660e\u89e3\u91ca\u5668\uff0cchmod +x amb2gjf\uff0c\u7136\u540e\u5c31\u53ef\u4ee5\u4f5c\u4e3a\u547d\u4ee4\u8c03\u7528\u4e86\u3002
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