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标题: 溶剂化遇到原子名称和力场规范不匹配问题怎么解决 [打印本页]

作者
Author: Jnannan 时间: 2025-10-25 12:14
标题: 溶剂化遇到原子名称和力场规范不匹配问题怎么解决
WARNING: Masses and atomic (Van der Waals) radii will be guessed
      based on residue and atom names, since they could not be
      definitively assigned from the information in your input
      files. These guessed numbers might deviate from the mass
      and radius of the atom type. Please check the output
      files if necessary. Note, that this functionality may
      be removed in a future GROMACS version. Please, consider
      using another file format for your input.

我的命令行，力场是AMBER99SB-ILDN protein, nucleic AMBER94 (Lindorff-Larsen et al., Proteins 78, 1950-58, 2010)
gmx pdb2gmx -f wt.clean.pdb -o wt.clean.gro -water tip4p
gmx editconf -f wt.clean.gro -o wt.gro -c -d 3.0 -bt cubic
gmx solvate -cp wt.gro -cs tip4p.gro -o wt_solv.gro -p topol.top

作者
Author: student0618 时间: 2025-10-25 12:58
本帖最后由 student0618 于 2025-10-25 15:57 编辑

这正常没大问题，担心的话VMD 打开检查一下水的位置。

作者
Author: Jnannan 时间: 2025-10-25 15:26
好滴，谢谢

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