{"id":78541,"date":"2026-02-27T21:48:47","date_gmt":"2026-02-27T13:48:47","guid":{"rendered":"https:\/\/www.wsisp.com\/helps\/78541.html"},"modified":"2026-02-27T21:48:47","modified_gmt":"2026-02-27T13:48:47","slug":"%e9%85%8d%e4%bd%93%e6%8b%93%e6%89%91%e6%96%87%e4%bb%b6%e7%9a%84%e8%87%aa%e5%8a%a8%e5%8c%96%e5%b7%a5%e5%85%b7acpype%e7%9a%84%e5%ae%89%e8%a3%85%e5%8f%8a%e4%bd%bf%e7%94%a8","status":"publish","type":"post","link":"https:\/\/www.wsisp.com\/helps\/78541.html","title":{"rendered":"\u914d\u4f53\u62d3\u6251\u6587\u4ef6\u7684\u81ea\u52a8\u5316\u5de5\u5177ACPYPE\u7684\u5b89\u88c5\u53ca\u4f7f\u7528"},"content":{"rendered":"<p>\u00a0\u672c\u6587\u4ecb\u7ecdGromacs\/Amber\u5206\u5b50\u52a8\u529b\u5b66\u6a21\u62df\u914d\u4f53\u53c2\u6570\u5316\u7a0b\u5e8facpype\u7684\u5b89\u88c5\u3001\u4f7f\u7528\u53ca\u6ce8\u610f\u4e8b\u9879\u3002<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" alt=\"\" height=\"418\" src=\"https:\/\/www.wsisp.com\/helps\/wp-content\/uploads\/2026\/02\/20260227134846-69a1a0be276b8.png\" width=\"1083\" \/><\/p>\n<p>ACPYPE&#xff08;A CPYthon Environment&#xff09;\u662f\u4e00\u4e2a\u7528\u4e8e\u4e3a\u5c0f\u5206\u5b50&#xff08;\u5982\u836f\u7269\u914d\u4f53&#xff09;\u751f\u6210 AMBER \u548c GROMACS \u517c\u5bb9\u62d3\u6251\u6587\u4ef6\u7684\u81ea\u52a8\u5316\u5de5\u5177\u3002\u5b83\u57fa\u4e8e Antechamber&#xff08;\u6765\u81ea AmberTools&#xff09;\u548c GAFF&#xff08;General AMBER Force Field&#xff09;&#xff0c;\u662f GROMACS \u7528\u6237\u5904\u7406\u975e\u6807\u51c6\u6b8b\u57fa&#xff08;\u5c24\u5176\u662f\u914d\u4f53&#xff09;\u6700\u5e38\u7528\u7684\u65b9\u6cd5\u4e4b\u4e00\u3002<\/p>\n<hr \/>\n<h3>\u4e00\u3001ACPYPE \u7684\u4f5c\u7528<\/h3>\n<p>\u5c06\u5c0f\u5206\u5b50&#xff08;\u901a\u5e38\u4e3a .mol2 \u6216 .sdf \u683c\u5f0f&#xff09;\u8f6c\u6362\u4e3a&#xff1a;<\/p>\n<ul>\n<li>AMBER \u683c\u5f0f&#xff1a;prmtop &#043; inpcrd<\/li>\n<li>GROMACS \u683c\u5f0f&#xff1a;top &#043; itp &#043; gro<\/li>\n<\/ul>\n<p>\u5e76\u81ea\u52a8\u5b8c\u6210&#xff1a;<\/p>\n<ul>\n<li>\u539f\u5b50\u7c7b\u578b\u5206\u914d&#xff08;GAFF&#xff09;<\/li>\n<li>\u7535\u8377\u8ba1\u7b97&#xff08;\u9ed8\u8ba4 AM1-BCC&#xff09;<\/li>\n<li>\u952e\/\u89d2\/\u4e8c\u9762\u89d2\u53c2\u6570\u5316<\/li>\n<li>\u62d3\u6251\u6587\u4ef6\u683c\u5f0f\u8f6c\u6362<\/li>\n<\/ul>\n<hr \/>\n<h3>\u4e8c\u3001\u5b89\u88c5 ACPYPE<\/h3>\n<h4>\u65b9\u6cd5 1&#xff1a;\u901a\u8fc7 conda&#xff08;\u63a8\u8350&#xff09;<\/h4>\n<p># \u5b89\u88c5 AmberTools&#xff08;\u5305\u542b antechamber&#xff09;\u548c acpype<br \/>\nconda create -n acpype -c conda-forge ambertools acpype openbabel<br \/>\nconda activate acpype<\/p>\n<p>\u2705 \u6b64\u65b9\u6cd5\u81ea\u52a8\u89e3\u51b3\u4f9d\u8d56&#xff08;\u5305\u62ec antechamber, parmchk2, tleap \u7b49&#xff09;<\/p>\n<h4>\u65b9\u6cd5 2&#xff1a;pip \u5b89\u88c5&#xff08;\u9700\u624b\u52a8\u5b89\u88c5 AmberTools&#xff09;<\/h4>\n<p>pip install acpype<\/p>\n<p>\u4f46\u5fc5\u987b\u5148\u5b89\u88c5 AmberTools&#xff08;\u4ece https:\/\/ambermd.org\/ \u83b7\u53d6&#xff09;\u6216\u8005\u5b89\u88c5Amber&#xff0c;\u5426\u5219\u65e0\u6cd5\u8fd0\u884c\u3002<\/p>\n<p>Amber24\u5b89\u88c5\u8bf7\u53c2\u8003\u535a\u6587&#xff1a;Amber\u5206\u5b50\u52a8\u529b\u5b66\u6a21\u62df1&#xff1a;Amber24\u7684\u5b89\u88c5<\/p>\n<hr \/>\n<h3>\u4e09\u3001\u4f7f\u7528\u6d41\u7a0b&#xff08;\u4ee5\u914d\u4f53\u4e3a\u4f8b&#xff09;<\/h3>\n<p>\u5047\u8bbe\u4f60\u6709\u4e00\u4e2a\u914d\u4f53\u6587\u4ef6 ligand.sdf&#xff08;\u6216 .mol2&#xff09;<\/p>\n<h4>\u6b65\u9aa4 1&#xff1a;\u51c6\u5907\u5e26\u7535\u8377\u7684 mol2 \u6587\u4ef6&#xff08;\u53ef\u9009\u4f46\u63a8\u8350&#xff09;<\/h4>\n<p>\u867d\u7136 acpype \u53ef\u8c03\u7528 antechamber \u8ba1\u7b97\u7535\u8377&#xff0c;\u4f46\u5efa\u8bae\u663e\u5f0f\u6307\u5b9a&#xff1a;<\/p>\n<p># \u4f7f\u7528 Open Babel \u8f6c\u6362\u683c\u5f0f&#xff08;\u4fdd\u7559\u6c22&#xff09;<br \/>\nobabel ligand.sdf -O ligand_h.mol2 -xh<\/p>\n<p># \u4f7f\u7528 antechamber \u8ba1\u7b97 AM1-BCC \u7535\u8377&#xff08;\u66f4\u53ef\u9760&#xff09;<br \/>\nantechamber -i ligand_h.mol2 -fi mol2 \\\\<br \/>\n            -o ligand_bcc.mol2 -fo mol2 \\\\<br \/>\n            -c bcc -s 2 -nc 0   # -nc: \u51c0\u7535\u8377&#xff08;\u5982 -1, 0, &#043;1&#xff09;<\/p>\n<p>\u26a0\ufe0f \u52a1\u5fc5\u786e\u8ba4\u914d\u4f53\u51c0\u7535\u8377&#xff08;\u5982\u7fa7\u9178\u53bb\u8d28\u5b50\u5316\u4e3a -1&#xff0c;\u80fa\u8d28\u5b50\u5316\u4e3a &#043;1&#xff09;<\/p>\n<h4>\u6b65\u9aa4 2&#xff1a;\u8fd0\u884c ACPYPE<\/h4>\n<p>acpype -i ligand_bcc.mol2 -o gmx -d<\/p>\n<h5>\u5e38\u7528\u9009\u9879&#xff1a;<\/h5>\n<table>\n<tr>\u9009\u9879\u8bf4\u660e<\/tr>\n<tbody>\n<tr>\n<td>-i<\/td>\n<td>\u8f93\u5165\u6587\u4ef6&#xff08;.mol2, .sdf, .pdb&#xff09;<\/td>\n<\/tr>\n<tr>\n<td>-o gmx<\/td>\n<td>\u8f93\u51fa GROMACS \u683c\u5f0f&#xff08;\u9ed8\u8ba4&#xff09;&#xff1b;-o amb \u8f93\u51fa AMBER \u683c\u5f0f<\/td>\n<\/tr>\n<tr>\n<td>-d<\/td>\n<td>\u5220\u9664\u4e34\u65f6\u6587\u4ef6&#xff08;\u53ef\u9009&#xff09;<\/td>\n<\/tr>\n<tr>\n<td>-n &lt;charge&gt;<\/td>\n<td>\u6307\u5b9a\u51c0\u7535\u8377&#xff08;\u82e5 mol2 \u4e2d\u672a\u6b63\u786e\u6807\u6ce8&#xff09;<\/td>\n<\/tr>\n<tr>\n<td>-a<\/td>\n<td>\u4f7f\u7528 AM1-BCC \u7535\u8377&#xff08;\u5373\u4f7f\u8f93\u5165\u5df2\u6709\u7535\u8377&#xff09;<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>\u8f93\u51fa\u6587\u4ef6&#xff08;\u5047\u8bbe\u914d\u4f53\u540d\u4e3a LIG&#xff09;&#xff1a;<\/p>\n<ul>\n<li>ligand_bcc_GMX.top<\/li>\n<li>ligand_bcc_GMX.itp<\/li>\n<li>ligand_bcc_GMX.gro<\/li>\n<li>ligand_bcc_AC.inpcrd \/ .prmtop&#xff08;AMBER \u683c\u5f0f&#xff09;<\/li>\n<\/ul>\n<hr \/>\n<h3>\u56db\u3001\u6574\u5408\u5230 GROMACS \u86cb\u767d-\u914d\u4f53\u6a21\u62df\u4e2d<\/h3>\n<li>\n<p>\u7f16\u8f91\u4e3b\u62d3\u6251\u6587\u4ef6 topol.top&#xff1a;<\/p>\n<p>\u5728 [ system ] \u4e4b\u524d\u6dfb\u52a0&#xff1a;<\/p>\n<p> #include &#034;ligand_bcc_GMX.itp&#034;\n <\/li>\n<li>\n<p>\u5728 [ molecules ] \u90e8\u5206\u6dfb\u52a0\u914d\u4f53&#xff1a;<\/p>\n<p> Protein_chain_A    1<br \/>\nLIG                1<\/p>\n<p>\u540d\u79f0 LIG \u5fc5\u987b\u4e0e .itp \u6587\u4ef6\u4e2d [ moleculetype ] LIG \u4e00\u81f4<\/p>\n<\/li>\n<li>\n<p>\u5408\u5e76\u5750\u6807\u6587\u4ef6&#xff1a;<\/p>\n<ul>\n<li>\u5c06\u86cb\u767d\u7684 .gro \u4e0e ligand_bcc_GMX.gro \u5408\u5e76<\/li>\n<li>\u624b\u52a8\u4fee\u6b63\u7b2c\u4e00\u884c\u7684\u603b\u539f\u5b50\u6570<\/li>\n<\/ul>\n<p>\u6216\u4f7f\u7528\u811a\u672c\/VMD\u786e\u4fdd\u5750\u6807\u65e0\u91cd\u53e0\u3002<\/p>\n<\/li>\n<hr \/>\n<h3>\u4e94\u3001\u5e38\u89c1\u95ee\u9898\u4e0e\u89e3\u51b3\u65b9\u6848<\/h3>\n<h4>\u274c \u95ee\u9898 1&#xff1a;&#034;Error: cannot run antechamber&#034;<\/h4>\n<p>\u539f\u56e0&#xff1a;AmberTools \u672a\u5b89\u88c5\u6216\u4e0d\u5728 PATH \u89e3\u51b3&#xff1a;\u7528 conda \u5b89\u88c5 ambertools&#xff0c;\u6216 source Amber \u73af\u5883<\/p>\n<p>source $AMBERHOME\/amber.sh  # \u5982\u679c\u4ece\u6e90\u7801\u5b89\u88c5<\/p>\n<hr \/>\n<h4>\u274c \u95ee\u9898 2&#xff1a;&#034;FATAL: Atom &#8230; does not have a type&#034;<\/h4>\n<p>\u539f\u56e0&#xff1a;GAFF \u65e0\u6cd5\u8bc6\u522b\u67d0\u4e9b\u7279\u6b8a\u539f\u5b50&#xff08;\u5982\u91d1\u5c5e\u3001\u787c\u7b49&#xff09; \u89e3\u51b3&#xff1a;<\/p>\n<ul>\n<li>\u68c0\u67e5\u5206\u5b50\u7ed3\u6784\u662f\u5426\u5408\u7406<\/li>\n<li>\u624b\u52a8\u7f16\u8f91 .mol2 \u4e2d\u7684\u539f\u5b50\u7c7b\u578b&#xff08;\u5982 du \u2192 c3&#xff09;<\/li>\n<li>\u8003\u8651\u4f7f\u7528 CGenFF&#xff08;CHARMM&#xff09;\u6216 Open Force Field<\/li>\n<\/ul>\n<hr \/>\n<h4>\u274c \u95ee\u9898 3&#xff1a;\u7535\u8377\u4e0d\u6b63\u786e&#xff08;\u5982\u4e2d\u6027\u5206\u5b50\u5e26\u7535&#xff09;<\/h4>\n<p>\u539f\u56e0&#xff1a;\u8f93\u5165\u6587\u4ef6\u672a\u6307\u5b9a\u8d28\u5b50\u5316\u72b6\u6001 \u89e3\u51b3&#xff1a;<\/p>\n<ul>\n<li>\u7528 Molecular Operating Environment (MOE)\u3001Epik&#xff08;Schr\u00f6dinger&#xff09;\u3001PROPKA \u6216 Avogadro \u9884\u5148\u4f18\u5316\u8d28\u5b50\u5316\u72b6\u6001<\/li>\n<li>\u663e\u5f0f\u6307\u5b9a -nc \u53c2\u6570&#xff1a; acpype -i lig.pdb -n 0 -o gmx\n <\/li>\n<\/ul>\n<hr \/>\n<h4>\u274c \u95ee\u9898 4&#xff1a;\u4e8c\u9762\u89d2\u53c2\u6570\u7f3a\u5931&#xff08;parmchk2 \u62a5 warning&#xff09;<\/h4>\n<p>\u539f\u56e0&#xff1a;GAFF \u5bf9\u67d0\u4e9b\u5b98\u80fd\u56e2\u8986\u76d6\u4e0d\u5168 \u89e3\u51b3&#xff1a;<\/p>\n<ul>\n<li>\u67e5\u770b\u751f\u6210\u7684 ligand.frcmod \u6587\u4ef6<\/li>\n<li>\u624b\u52a8\u8865\u5145\u7f3a\u5931\u53c2\u6570&#xff08;\u9700\u91cf\u5b50\u5316\u5b66\u8ba1\u7b97\u6216\u53c2\u8003\u7c7b\u4f3c\u5206\u5b50&#xff09;<\/li>\n<\/ul>\n<hr \/>\n<h3>\u516d\u3001\u9a8c\u8bc1\u62d3\u6251\u662f\u5426\u5408\u7406<\/h3>\n<li>\n<p>\u68c0\u67e5 .itp \u6587\u4ef6&#xff1a;<\/p>\n<ul>\n<li>\u539f\u5b50\u7c7b\u578b\u662f\u5426\u5408\u7406&#xff08;\u5982 c3, os, n&#xff09;<\/li>\n<li>\u7535\u8377\u603b\u548c\u662f\u5426\u7b49\u4e8e\u9884\u671f\u51c0\u7535\u8377<\/li>\n<\/ul>\n<\/li>\n<li>\n<p>\u77ed\u65f6\u95f4 MD \u6d4b\u8bd5&#xff1a;<\/p>\n<p> gmx grompp -f minim.mdp -c ligand.gro -p ligand.top -o test.tpr<br \/>\ngmx mdrun -v -deffnm test<\/p>\n<p>\u82e5\u62a5 \u201cblowing up\u201d \u6216 LINCS error&#xff0c;\u8bf4\u660e\u529b\u573a\u53c2\u6570\u6709\u95ee\u9898\u3002<\/p>\n<\/li>\n<li>\n<p>\u5bf9\u6bd4\u91cf\u5b50\u529b\u5b66&#xff08;QM&#xff09;\u51e0\u4f55\u7ed3\u6784&#xff08;\u9ad8\u7ea7&#xff09;&#xff1a;<\/p>\n<ul>\n<li>\u4f18\u5316\u914d\u4f53 QM \u6784\u578b&#xff08;\u5982 B3LYP\/6-31G*&#xff09;<\/li>\n<li>\u4e0e MM \u4f18\u5316\u7ed3\u6784 RMSD \u6bd4\u8f83&#xff08;\u5e94 &lt; 0.5 \u00c5&#xff09;<\/li>\n<\/ul>\n<\/li>\n<hr \/>\n<h3>\u4e03\u3001\u66ff\u4ee3\u65b9\u6848&#xff08;\u5f53 ACPYPE \u4e0d\u9002\u7528\u65f6&#xff09;<\/h3>\n<table>\n<tr>\u5de5\u5177\u529b\u573a\u7279\u70b9<\/tr>\n<tbody>\n<tr>\n<td>CGenFF<\/td>\n<td>CHARMM<\/td>\n<td>\u9002\u5408\u542b\u82b3\u9999\/\u6742\u73af\u5206\u5b50&#xff0c;\u9700\u624b\u52a8\u6821\u6b63<\/td>\n<\/tr>\n<tr>\n<td>SwissParam<\/td>\n<td>CHARMM<\/td>\n<td>\u5728\u7ebf\u670d\u52a1\u5668&#xff0c;\u5feb\u901f\u4f46\u5206\u5b50\u5e93\u6709\u9650<\/td>\n<\/tr>\n<tr>\n<td>Open Force Field &#043; ParmEd<\/td>\n<td>SMIRNOFF<\/td>\n<td>\u65b0\u4e00\u4ee3\u529b\u573a&#xff0c;\u7cbe\u5ea6\u9ad8&#xff0c;\u652f\u6301 GROMACS<\/td>\n<\/tr>\n<tr>\n<td>antechamber &#043; parmed<\/td>\n<td>GAFF<\/td>\n<td>\u624b\u52a8\u6d41\u7a0b&#xff0c;\u66f4\u7075\u6d3b<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<hr \/>\n<h3>\u516b\u3001\u603b\u7ed3<\/h3>\n<p>ACPYPE \u662f GROMACS \u7528\u6237\u5904\u7406\u914d\u4f53\u7684\u9996\u9009\u5de5\u5177&#xff0c;\u524d\u63d0\u662f&#xff1a;<\/p>\n<ul>\n<li>\u5206\u5b50\u4e0d\u542b\u7f55\u89c1\u5143\u7d20<\/li>\n<li>\u8d28\u5b50\u5316\u72b6\u6001\u5df2\u77e5<\/li>\n<li>\u63a5\u53d7 GAFF \u529b\u573a\u7684\u8fd1\u4f3c\u6027<\/li>\n<\/ul>\n<p>&#x1f4cc;\u6700\u4f73\u5b9e\u8df5&#xff1a;<\/p>\n<li>\u7528 ChemDraw \/ MOE \u51c6\u5907\u6b63\u786e\u8d28\u5b50\u5316\u7ed3\u6784<\/li>\n<li>\u5bfc\u51fa\u4e3a .mol2 \u5e76\u7528 antechamber \u8ba1\u7b97 AM1-BCC \u7535\u8377<\/li>\n<li>\u7528 acpype -o gmx 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