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[求助]
topol文件不识别小分子 已有1人参与
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最近刚刚学gromacs，按照网上的tutorial步骤走遇到一个问题就是我要添加我的小分子到pdb2gmx产生的conf.gro文件，我按照网上的tutorial添加需要的文件之后，还是不识别我的小分子，怎么办？我把topol文件里面的分子数手动修改之后，就出现下面的错误了 NOTE 1 [file topol.top, line 10673]: System has non-zero total charge: 6.000001e+00 Warning: atom name 1694 in topol.top and solv.gro does not match (CAA - AA) Warning: atom name 1695 in topol.top and solv.gro does not match (CAG - AG) Warning: atom name 1696 in topol.top and solv.gro does not match (CAH - AH) Warning: atom name 1697 in topol.top and solv.gro does not match (CAJ - AJ) Warning: atom name 1698 in topol.top and solv.gro does not match (CAF - AF) Warning: atom name 1699 in topol.top and solv.gro does not match (HAG - AG) Warning: atom name 1700 in topol.top and solv.gro does not match (CAD - AD) Warning: atom name 1701 in topol.top and solv.gro does not match (HAE - AE) Warning: atom name 1702 in topol.top and solv.gro does not match (CAC - AC) Warning: atom name 1703 in topol.top and solv.gro does not match (HAD - AD) Warning: atom name 1704 in topol.top and solv.gro does not match (CAE - AE) Warning: atom name 1705 in topol.top and solv.gro does not match (HAF - AF) Warning: atom name 1706 in topol.top and solv.gro does not match (CAI - AI) Warning: atom name 1707 in topol.top and solv.gro does not match (OAB - AB) Warning: atom name 1708 in topol.top and solv.gro does not match (HAL - AL) WARNING 1 [file topol.top, line 10673]: 15 non-matching atom names atom names from topol.top will be used atom names from solv.gro will be ignored NOTE 2 [file topol.top]: The largest charge group contains 11 atoms. Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts. For efficiency and accuracy, charge group should consist of a few atoms. For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc. Analysing residue names: There are: 163 Protein residues There are: 1 Other residues There are: 10445 Water residues Analysing Protein... Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups... Number of degrees of freedom in T-Coupling group rest is 67791.00 Largest charge group radii for Van der Waals: 0.354, 0.287 nm Largest charge group radii for Coulomb: 0.354, 0.287 nm Calculating fourier grid dimensions for X Y Z Using a fourier grid of 72x72x72, spacing 0.109 0.109 0.109 Estimate for the relative computational load of the PME mesh part: 0.37 This run will generate roughly 383 Mb of data There were 2 notes There was 1 warning 这个怎么办？ |
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【答案】应助回帖
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感谢参与，应助指数 +1
蓝紫色玻璃心(金币+1): 2011-12-31 08:59:40
御剑江湖(金币+5): 谢谢 2011-12-31 17:51:48
感谢参与，应助指数 +1
蓝紫色玻璃心(金币+1): 2011-12-31 08:59:40
御剑江湖(金币+5): 谢谢 2011-12-31 17:51:48
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There was 1 warning 这个warning可以忽略不管，因为： atom names from topol.top will be used atom names from solv.gro will be ignored 我在做模拟的时候，也遇到过类似的问题，这个warning忽略掉不会影响。在后续的模拟中，就不会提示了。 There were 2 notes 第一个notes的意思是你的体系没有电中性，你的 系统带有6e个电荷 因此你需要给系统添加 -6e个电荷 |
3楼2011-12-30 22:32:15