CASEA的奇思妙想

Amber HBond

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Amber 使用cpptraj 分析轨迹之HBond氢键计算

Hbond

Example

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parm xxx.parm7
trajin xxx.crd
# 计算残基1-22间所有氢键，输出氢键数到nhb.dat，氢键信息到avghb.dat
hbond :1-22 out nhb.dat avgout avghb.dat
# 残基1上的供体残基2上的受体形成的氢键
hbond donormask :1 acceptormask :2 out nhb.dat avgout avghb.dat
# 搜寻分子内溶质-溶剂氢键，并保存氢键时间序列
hbond HB out nhb.dat avgout solute_avg.dat solventacceptor :WAT@O solventdonor :WAT solvout solvent_avg.dat bridgeout bridge.dat series uuseries uuhbonds.agr uvseries uvhbonds.agr
# 寻找溶质和Na+离子之间形成的非特异性氢键
hbond HB-Ion out nhb.agr avgout ion_avg.dat solventacceptor :Na+ solventdonor :Na+
run

Command

使用几何标准计算氢键

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hbond [<dsname>] [out <filename>] [<mask>] [angle <acut>] 
      [dist <dcut>][donormask <dmask>] [donorhmask <dhmask>]
      [acceptormask <amask>] [avgout <filename>] 
      [printatomnum] [nointramol] [image]
      [solventdonor <sdmask>] [solventacceptor <samask>]
      [solvout <filename>] [bridgeout <filename>]
      [series [uuseries <filename>] [uvseries <filename>]]
  • [<dsname>] 数据集名
  • [out <filename>] 输出文件
  • [<mask>] 用于寻找溶质氢键受/供体的原子范围
  • [angle <acut>] 氢键键角截断(default 135°). 指定-1禁用
  • [dist <dcut>] 氢键距离截断 (受体到供体重原子, default 3.0 Å).
  • [donormask <dmask>] 使用dmask中的原子作为溶质供体重原子；如donorhmask不指定，只有与氢成键原子被考虑为供体
  • [donorhmask <dhmask>] 使用dmask中的原子作为溶质供体氢原子；只有donormask指定时才指定。donormask和donorhmask必须一一对应。
  • [acceptormask <amask>] 溶质受体
  • [avgout <filename>] 输出溶质-溶质间平均氢键
  • [printatomnum] 除了残基名、编号、原子名外还输出原子序号
  • [nointramol] 忽略分子内氢键
  • [image] 打开距离/角度image
  • [solventdonor <sdmask>] 溶剂供体
  • [solventacceptor <samask>] 溶剂受体
  • [solvout <filename>] 输出溶剂-溶质间平均氢键
  • [bridgeout <filename>] 输出检测到的水桥
  • [series] 对于所有检测到的氢键保存每帧氢键的成键信息；溶质-溶质氢键被保存为[solutehb];溶质-溶剂氢键保存为[solventhb]；[uuseries ] 输出溶质-溶质氢键时间序列；[uvseries ]输出溶质-溶剂氢键时间序列；

Data Sets

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<dsname>[UU] Number of solute-solute hydrogen bonds.
<dsname>[UV] (only for solventdonor/solventacceptor) Number of solute-solvent hydrogen bonds.
<dsname>[Bridge] (only for solventdonor/solventacceptor) Number of bridging solvent molecules.
<dsname>[ID] (only for solventdonor/solventacceptor) String identifying bridging solvent residues and the solute residues they bridge.
<dsname>[solutehb] (series only) Time series for solute-solute hydrogen bonds; 1 for present, 0 for not present.
<dsname>[solventhb] (series only) Time series for solute-solvent hydrogen bonds; 1 for present, 0 for not present.