amber坐标文件转换为pdb格式

In the SwissPDB Viewer, there is an option called “aa making clashes” under the “Select” menu. This command will highlight the amino acid residues that are making bad contacts with its neighbors. To visualize the clashes, choose “by selection” from the “Color” menu.

# cpptraj基本教程

cpptraj -i rmsd.cpptraj > rmsd.log
cpptraj -p file.prmtop -y file.mdcrd -tl # 查看轨迹文件的帧数

## 注意

• help command eg help distance
• 扩展名可以决定输出文件的类型
• select # 将会显示选中部分的原子index
• parm file_name # 拓扑文件可以是.parm7, pdb, mol2, cif, psf, sdf, arc,甚至是gmx的top
• trajin file_name # 轨迹文件可以是pdb, mol2, gro, trr等多种格式
• cpptraj.OMP, cpptraj.MPI
为了使用openMP，configure的时候应加上-openmp 选项
We can easily tell if cpptraj has been compiled with OpenMP as it will print OpenMP in the title, and/or by calling cpptraj --defines and looking for -D_OPENMP.

cpptraj 选项

## symmrmsd 考虑对称性的rmsd

Perform symmetry-corrected RMSD calculation. This is done by identifying potential symmetric atoms in each
residue, performing an initial best-fit, then determining which configuration of symmetric atoms will give the
lowest RMSD using atomic distance to reference atoms.

## 测量距离，角度

You may need to go through the files and manually adjust any sections where the angle has jumped from -180 to +180 so that it looks clean when plotted, I won’t go into details on how to do this here but suffice to say you can do it in xmgrace with some code like:

# top, 轨迹去水(离子, 其它原子)

## top文件去水，使用 CPPTRAJ 或者 parmed.py

### 使用cpptraj

parmstrip [parm | parmindex <#> | <#>]

# cpptraj基础教程2

## autoimage

[firstatom] 选项: Image based on molecule first atom; default is to image by molecule center of mass.

## image

For periodic systems only, image molecules/residues/atoms that are outside of the box back into the box.

## 重设 box center

Move all atoms so that the center of the atoms in is centered at the specified location: box center (default), coordinate origin, or reference coordinates

## average

closest 10 :1-151 first closestout closestmols.dat outprefix closest

## energy

Calculate the energy for atoms in .

## lie

Periodic topologies and trajectories are required (i.e., explicit solvent is necessary
A separate electrostatic and van derWaals cutoff can be applied, the default is 12.0 Angstroms for both

# 氢键分析

A … H - D
A和D一般都默认为 FON
A hydrogen bond is defined as being between an acceptor heavy atom A, a donor hydrogen atom H, and a donor heavy atom D. If the A to D distance is less than the distance cutoff and the A-H-D angle is greater than the angle cutoff a hydrogen bond is considered formed. Imaging of distances/angles is not performed by default, but can be turned on using the image keyword.

They are formed when a single hydrogen atom is effectively shared between the heavy atom it is covalently bonded to (the hydrogen bond donor) and another heavy atom (the hydrogen bond acceptor). Both the donor and acceptor atoms are typically quite electronegative.

CPPTRAJ will also track solute to solvent hydrogen bonds and solvent bridging interactions (i.e. two or more solute residues hydrogen bonded to a single solvent residue).

Hydrogen bond is formed when A to D distance < dcut and A-H-D angle > acut; if acut < 0 it is ignored.

eg.

hbond :1-22 out nhb.dat avgout avghb.dat

To search for all intermolecular hydrogen bonds only and solute-solvent hydrogen bonds, saving time series data to HB:

To search for non-specific hydrogen bonds between solute and ions named Na+:

# atom selection

Bug: 无法区分 alpha carbon CA and a calcium ion Ca

# Cluster Analysis using the MMTSB Toolset

## pdb重新编号(将 1,10,100变成001,010,100)

教程里有对应脚本，不如自己写一个

## Do the clustering

Remove first line since kclust can only handle < 50000 structures. We will fit structures 2 to 50,000. We need to remember that we did this as it means our pdbs actually start counting from two. This means that the ID’s in the centroid files will be off by one. You will see what I mean later. Here is the clustfils file.

• Centroid_6 文件内容
• 97 trp.pdb.00098 5.221610 # ID member_of_this_centroid
• rmsd_distance_from_its_centroid
• the centeroid in pdb format

## Process the Clusters

• 使用脚本 extract_centroids.awk 提取出每个聚类的成员及其中心结构
• 查看与聚类中心最接近的结构的编号