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注册: 2010-03-17
专业: 化学计量学与化学信息学

[求助] topol文件不识别小分子已有1人参与

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

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这个怎么办？

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