Trajectory Analysis using Bio3D.txt

#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 and DCD 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(protlig_pdb, protlig_dcd, fit=TRUE, ncore=1) #change the "ncore" if you have multiple cores available 
> 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(protlig_dcd)
> plot(rf, ylab="RMSF (Å)",xlab="Residue")
> dev.copy(jpeg,filename="rmsf.jpg")
> dev.off()

#Principal component Analysis (PCA)

> pc<-pca.xyz(protlig_dcd)
> plot(pc,col=bwr.colors(nrow(dcd)))
> dev.copy(jpeg, filename="pca,jpg")
> dev.off()

#Dynamic Cross-Correlation Matrix (DCCM)

> dc<-dccm.xyz(protlig_dcd)
> plot.dccm(dc)