MD-Trajectory-Analysis-Bio3D

Introduction

This repository contains documentation and example scripts for performing molecular dynamics (MD) trajectory analysis using the Bio3D package in R. Bio3D is an R package that provides tools for the analysis of biomolecular structure, sequence, and molecular dynamics trajectories.

After a successful MD simulation, Create a new folder named analysis within the working folder

mkdir analysis

cd analysis

Trajectory correction

gmx trjconv -s ../md.tpr -f ../md.xtc -o md_center.xtc -center -pbc mol -ur compact

Select: protein

Select: system

collect the initial structure

gmx trjconv -s ../md.tpr -f ../md.xtc -o md.gro -pbc mol -ur compact -center -dump 0

select: protein

select: system

gmx trjconv -s ../md.tpr -f ../md.xtc -o md.pdb -pbc mol -ur compact -center -dump 0

select: protein

select: system (or)

gmx editconf -f md.gro -o md.pdb

[Note: you can either convert md.gro into md.pdb using gmx editconf, or directly download the md.pdb from the trajectory using -dump 0 as above mentioned]

Trajectory conversion

mdconvert md_center.xtc -t md.gro -o md.dcd

Required files prior to do analysis using Bio3D

1. md.dcd
2. md.pdb

Bio3D installation

install.packages("bio3d", dependencies=TRUE)

library(bio3d)

Trajectory Preparation

pdb<-read.pdb("md.pdb")

dcd<-read.dcd("md.dcd", cell=FALSE)

Select CA atoms of the protein

ca.inds<-atom.select(pdb,"protein",elety="CA")

Fit the trajectory to the selection of protein atoms

trj<-fit.xyz(pdb$xyz, dcd, fixed.inds=ca.inds$xyz, mobile.inds=ca.inds$xyz)

Trim the PDB to include only the selected protein CA atoms

protpdb<-trim.pdb(pdb,ca.inds)

protdcd<-trim(trj, col.inds=ca.inds$xyz)

Print the trimmed PDB coordinates

print(protpdb$xyz)

Print the trimmed trajectory coordinates

print(protdcd)

Trajectory Analysis

RMSD

rd<-rmsd(protpdb, protdcd, fit=TRUE, ncore=1)

plot(rd, typ='l',ylab="RMSD (Å)",xlab="Frame No.")

points(lowess(rd), typ='l', col="red", lty=1, lwd=3)

dev.copy(jpeg,filename="rmsd.jpg")

dev.off()

RMSF

rf<-rmsf(protdcd)

plot(rf, ylab="RMSF (Å)",xlab="Residue")

dev.copy(jpeg,filename="rmsf.jpg")

dev.off()

Principal Component Analysis (PCA)

pc<-pca.xyz(protdcd)

plot(pc,col=bwr.colors(nrow(dcd)))

dev.copy(jpeg, filename="pca,jpg")

dev.off()

Dynamic Cross Correlation Matrix (DCCM)

dc<-dccm.xyz(protdcd)

plot.dccm(dc)

Acknowledgements

The MD-Trajectory-Analysis-Bio3D was documented by Mohamed Asif. 

Feel free to contribute, report issues, or suggest enhancements by creating a GitHub Issue or submitting a pull request.

Enjoy analyzing molecular dynamics trajectories with Bio3D! 😉

Citation

1. Grant, B. J., Skjærven, L., & Yao, X. (2020). The Bio3D packages for structural bioinformatics. Protein Science, 30(1), 20–30. https://doi.org/10.1002/pro.3923