cpptraj教程-02

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本文内容摘抄或翻译自AMBER手册或教程，为本人学习AMBER时的笔记，如有侵权请联系删除。 ** lifetime vector cluster matrix diagmatrix 对角化矩阵，求特征值，特征向量 modes 分析特征模式 **

pdb文件中有三个残基合在一起，当作非标准氨基酸来处理

输入文件为.cif格式，从pdb网站下载 antechamber -fi ccif -i CRO.cif -bk CRO -fo ac -o cro.ac -c bcc -at amber

dna接上小分子

Tutorial A1: Setting up a DNA-Ligand System

PCA分析

TUTORAL C3: Introduction to Principal Component Analysis with CPPTRAJ

聚类分析

TUTORAL C4: Combined Clustering Analysis with CPPTRAJ

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writedata end-to-end.dat end-to-end   # 保存为标准的文本格式

avg 计算均值，方差

readdata perres.peptide.dat avg perres.peptide.dat out output.dat name V

hist

对一维数据进行hist建议输出.agr格式文件，二维hist建议输出.gnu格式文件 

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dihedral phi :2@C :3@N :3@CA :3@C
dihedral psi :3@N :3@CA :3@C :4@N
hist phi,-180,180,*,72 psi,-180,180,*,72 out hist.gnu    # *号表示此数据由已知数据计算而得

dihedral psi :3@N :3@CA :3@C :4@N
hist psi,-100,0,*,72 out hist.agr norm                   # norm the sum over all bins equals 1.0.
hist psi,-100,0,*,72 out hist.agr normint                # norm the integral over them is 1.0.

hist psi,-100,0,*,72 out hist.agr free 300               # 计算300K下的自由能 Gi=-RTln(Ni/Nmax)，Bins with no population are given an artificial barrier equivalent to a population of 0.5.

xmgrace 中由时间序列得到统计分布

参考教程(Introduction to Nucleic Acids simulations A-DNA to B-DNA transition) Data -> Transformations -> Histograms...

计算 average correlations between the motion of atoms in 

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atomiccorr [<mask>] out <filename> [cut <cutoff>] [min <min spacing>] [byatom | byres]

atomiccorr :1-13 out acorr.gnu byres

atommap

按连续编号对原子排序 

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fixatomorder [outprefix <name>]

setvelocity

按给定温度下的麦克斯韦分布设定速度

volume 计算盒子的体积

volume out vol.agr

分析工具

autocorr 计算自相关函数

autocorr [name ] [ ...] [out ] [lagmax ] [nocovar] [direct]

corr 计算自相关或者协相关

corr out [] [lagmax ] [nocovar] [direct]

crosscorr

Calculate the Pearson product-moment correlation coefficients between all specified datasets crosscorr [name ] [ ...] [out ]

curvefit 进行曲线拟合

integrate 对数据进行积分

meltcurve 计算融化曲线

Cartesian covariance matrix calculation and projection (PCA) (From amber16 manual)

  • Step one. Generate average structure. 
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    # RMS-Fit to first frame to remove global translation/rotation.
    parm myparm.parm7
    trajin mytraj.nc
    rms first !@H=
    average crdset AVG
    run
    # Step two. RMS-Fit to average structure. Calculate covariance matrix.
    # Save the fit coordinates.
    rms ref AVG !@H=
    matrix covar name MyMatrix !@H=
    createcrd CRD1
    run
    # Step three. Diagonalize matrix.
    runanalysis diagmatrix MyMatrix vecs 2 name MyEvecs
    # Step four. Project saved fit coordinates along eigenvectors 1 and 2
    crdaction CRD1 projection evecs MyEvecs !@H= out project.dat beg 1 end 2

Dihedral covariance matrix calculation and projection for backbone phi/psi (PCA) (From amber16 manual)

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parm ../1rrb_vac.prmtop
trajin ../1rrb_vac.mdcrd
# Generation of phi/psi dihedral data
multidihedral BB phi psi resrange 2
run
# Calculate dihedral covariance matrix and obtain eigenvectors
matrix dihcovar dihedrals BB[*] out dihcovar.dat name DIH
diagmatrix DIH vecs 4 out modes.dihcovar.dat name DIHMODES
run
# Project along eigenvectors
projection evecs DIHMODES out dih.project.dat beg 1 end 4 dihedrals BB[*]
run