CASEA的奇思妙想

Amber 体系性质计算

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Amber 使用cpptraj 分析轨迹之密度、能量、扩散系数、回转半径等计算

Density

沿坐标计算体系密度

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density [out <filename>] [name <set name>] [delta <resolution>] 
        [x|y|z] [number|mass|charge|electron] 
        [efile <filename>] <mask1> ... <maskN>
#
density out number_density.dat number delta 0.25 ":1" ":WAT"
  • out 输出直方图：每个mask的相对距离-密度
  • delta 分辨率，决定柱状图数量(default 0.25 Å)
  • x|y|z 密度计算坐标 (default z)
  • number|mass|charge|electron 数量、质量、点电荷或电子密度
  • mask1 ... maskN 原子选择语句，可以多个。

Diffusion

计算分子的传质扩散

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diffusion [{out <filename> | separateout <suffix>}] 
          [time <time per frame>] [noimage] [<mask>] 
          [<set name>] [individual] [diffout <filename>] 
          [nocalc]
# 计算水中扩散
diffusion :WAT@O out WAT_O.agr WAT_O diffout DC.dat
  • [out <filename>] 输出均方根位移(MSD)
  • [separateout <suffix>] 输出MSD到指定后缀的文件
  • [time <time_per_frame>] 帧之间的时间尺度 ps；default is 1.0.
  • [noimage]
  • [<mask>] 计算扩散的原子，默认all
  • [<set name>] MSD data set name.
  • [individual] 输出mask中每个原子的扩散和平均扩散率
  • [diffout <filename>] 输出扩散常数
  • [nocalc] 不计算扩散常数

DataSet

[X] MSD(s) in the X direction.
[Y] MSD(s) in the Y direction.
[Z] MSD(s) in the Z direction.
[R] Overall MSD(s).
[A] Overall displacement(s).
[D] Diffusion constants.
[Label] Diffusion constant lablels.
[Slope] Linear regression slopes.
[Intercept] Linear refression Y-intercepts.
[Corr] Linear regression correlation coefficients.

Energy

计算简单的键长、键角、二面角和非间相互作用项

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energy [<name>] [<mask1>] [out <filename>] [bond] [angle] 
       [dihedral] [nb14] {[nonbond] | [elec] [vdw]} 
       [ etype {simple | directsum [npoints <N>] | ewald 
        [cut <cutoff>] [dsumtol  <dtol>] [rsumtol <rtol>] 
        [ewcoeff <coeff>] [skinnb <skinnb>] 
        [mlimits <X>,<Y>,<Z>]} ]
  • [<name>]数据集
  • [<mask1>] 用于计算能量的原子
  • [out <filename>] 输出文件
  • [bond] 计算成键能量
  • [angle] 计算键角能量
  • [dihedral] 计算二面角能量
  • [nb14] 计算nonbonded 1-4 能量
  • [nonbond] 计算非键能量(静电势及范德华力)
  • [elec] 计算静电势
  • [vdw] 计算范德华力
  • [etype <type>] 以指定类型计算经典
  • [simple] 简单库伦项计算经典，无截断
  • [directsum] 直接求和经典方法
  • [npoints <N>] 每个方向的分区数
  • [ewald] Ewald加合法
  • cut <cutoff> 直接空间截断 Angstroms (default 8.0).
  • dsumtol <dtol> 加和限度 (default 0.00001). 用于确定ewald系数
  • rsumtol <rtol> Reciprocal sum tolerance (default 0.00005). Used to determine number of reciprocal space vectors.
  • ewcoeff <coeff> Ewald coefficient in 1/Ang.
  • skinnb Used to determine pairlist atoms (added to cut, so pairlist cutoff is cut + skinnb); included in order to maintain consistency with results from sander.
  • mlimits <X>,<Y>,<Z> Explicitly set the number of reciprocal space vectors in each dimension.

DataSet Aspects

[bond] Bond energy.
[angle] Angle energy.
[dih] Dihedral energy.
[vdw14] 1-4 van der Waals energy.
[elec14] 1-4 electrostatic energy.
[vdw] van der Waals energy.
[elec] Electrostatic energy.
[total] Total energy.

Radgyr | Rog

计算回转半径

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radgyr [<name>] [<mask>] [out <filename>] 
       [mass] [nomax] [tensor]
# 计算残基4-10的非氢原子回转半径
radgyr :4-10&!(@H=) out rog.dat mass nomax
  • [<name>] 数据集
  • [<mask>] 计算回转半径的原子(默认all)
  • [out <filename>] 输出
  • [mass] 质量权重的回转半径
  • [nomax] 不计算最大回转半径
  • [tensor] 计算回转半径张量, output format ’XX YY ZZ XY XZ YZ’.

DataSet

<name> Radius of gyration in Ang.
<name>[Max] Max radius of gyration in Ang.
<name>[Tensor] Radius of gyration tensor; format ’XX YY ZZ XY XZ YZ’.

Radial | Rdf

计算径向分布函数(RDF)

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radial [out <outfilename>] <spacing> <maximum> <solvent mask1> 
       [<solute mask2>] [noimage] 
       [density <density> | volume] [<dataset name>]
       [intrdf <file>] [rawrdf <file>] 
       [{{center1|center2|nointramol} | [byres1] [byres2] 
        [bymol1] [bymol2]}]
  • <outfilename> 输出文件
  • <spacing> Bin 间距
  • <maximum> Max bin value, required.
  • <solvent mask1> Atoms to calculate RDF for, required.
  • [<solute mask2>] (Optional) If specified calculate RDF of all atoms in <solvent mask1> to each atom in <solute mask2>.
  • [noimage] Do not image distances.
  • [density <density>] Use density value of <density> for normalization (default 0.033456 molecules Å^3).
  • [volume] Determine density for normalization from average volume of input frames.
  • [center1] Calculate RDF from geometric center of atoms in <solvent mask1> to all atoms in <solute mask2>.
  • [center2] Calculate RDF from geometric center of atoms in <solute mask2> to all atoms in <solvent mask1>.
  • [nointramol] Ignore intra-molecular distances.
  • [intrdf <file>] Calculate integral of RDF bin values (averaged over # of frames but otherwise not normalized) and write to <file> (can be same as <output_filename>).
  • [rawrdf <file>] Write raw (non-normalized) RDF values to <file>.
  • [byres1] Calculate using the centers of mass of each residue in the first mask.
  • [bymol1] Calculate using the centers of mass of each molecule in the first mask.
  • [byres2] Calculate using the centers of mass of each residue in the second mask.
  • [bymol2] Calculate using the centers of mass of each molecule in the second mask.

dssp secstruct

使用dssp算法计算二级结构成分

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secstruct [<name>] [out <filename>] [<mask>] 
          [sumout <filename>][assignout <filename>] 
          [totalout <filename> [ptrajformat] [betadetail] 
          [namen <N name>] [nameh <H name>] 
          [nameca <CA name>][namec <C name>] [nameo <O name>]
  • [<name>] 数据集
  • [out <filename>] 输出二级结构-时间 文件
  • [<mask>] 计算二级结构涉及原子
  • [totalout <filename>] 输出每帧结构的二级结构成分
  • [sumout <sumfilename>] 输出平均二级结构涉及残基到<sumfilename>
  • [assignout <filename>] Write overall secondary structure assignment (based on dominant secondary structure type for each residue) to file.
  • [ptrajformat] 将每帧的二级结构作为字符串输出
  • [betadetail] Record anti-parallel beta and parallel beta in place of extended and bridge secondary structure. If a residue could be both only anti-parallel is reported.
  • [namen <N name>] 骨架酰胺氮原子名称 (default ’N’).
  • [nameh <H name>] 骨架酰胺氢原子名称 (default ’H’).
  • [nameca <CA name>] 骨架$\alpha$碳原子名称 (default ’CA’).
  • [namec <C name>] 骨架羰基碳原子名称 (default ’C’).
  • [nameo <O name>] 骨架羰基氧原子名称 (default ’O’).
  • [namesg <SG name>] 半胱氨酸硫原子名称 (default ‘SG’).

Data Sets Created:

<name>[res] 每帧残基二级结构；index对应残基序号；如果指定ptrajformat，这些将为字符串，否则为整数。
<name>[avgss] 每种二级结构的平均，index对应于二级结构类型
<name>[None] Total fraction of residues with no structure vs time.
<name>[Para] Total fraction of residues with parallel beta structure vs time.
<name>[Anti] Total fraction of residues with anti-parallel beta structure vs time.
<name>[3-10] Total fraction of 3-10 helical structure vs time.
<name>[Alpha] Total fraction of alpha helical structure vs time.
<name>[Pi] Total fraction of Pi helical structure vs time.
<name>[Turn] Total fraction of turn structure vs time.
<name>[Bend] Total fraction of bend structure vs time.

Character Integer DSSP Char SS type
0 0 ‘ ‘ None
b 1 ‘E’ Parallel Beta-sheet
B 2 ‘B’ Anti-parallel Beta-sheet
G 3 ‘G’ 3-10 helix
H 4 ‘H’ Alpha helix
I 5 ‘I’ Pi (3-14) helix
T 6 ‘T’ Turn
S 7 ‘S’ Bend

areapermol

计算指定平面中每个分子的面积

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areapermol [<name>] {[<mask1>] [nlayers <#>] | nmols <#>}
					 [out <filename>] [{xy | xz | yz}]
# 计算OL残基面积
areapermol OL_area :OL nlayers 2 out apm.dat
  • [<name>] 数据集
  • [<mask1>] 残基选择语句，如果选中残基中原子则选中整个残基
  • [nlayers <#>] 分子层数
  • [nmols <#>] 未指定残基选择语句，计算面积时使用的分子数
  • [out <filename>] 输出文件名
  • [{xy|xz|yz}] 计算面积的盒子横截面(default xy)

watershell

计算两个溶剂层之间的水分子数

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watershell <solutemask> [out <filename>] [lower <lower cut>] 
           [upper <upper cut>] [noimage] [<solventmask>]
  • <solutemask> 溶质原子选择
  • [out <filename>] 输出文件名
  • [lower <lower cut>] 第一水层截断 (default 3.4 Angstroms).
  • [upper <upper cut>] 第二水层截断 (default 5.0 Angstroms).
  • [noimage] Do not image distances.
  • [<solventmask>] 溶剂原子选择

Dataset

[lower] Number of solvent molecules in first solvent shell.
[upper] Number of solvent molecules in second solvent shell.