VMD

Scripting is done through the Tk console using tcl language.

This basic tutorial is recommended for understanding this section.

Align Molecules

Using Tk console:

*Using MultiSeq:*

Alignment is based on sequence similarity, so this procedure is meant to align different entries of the same sequence.

 

Merge Molecules

Use this code to create a PDB file of two merged protein structures (e.g. creating receptor-G protein complex)

 

Check for Atom Clashes

Find atom-atom conflicts to diagnose a potentially bad complex

Track Water Molecules in a Trajectory

Trajectory Clustering

1) Save trajectory snapshots as separate PDB files.

/home/exec/programs/mmtsb/toolset/perl/cluster.pl -centroid -centout clusterHead -kclust -radius 2.0 *.pdb > cluster2A.out

Obtain the Average Structure from a Trajectory

Hydrogen bond analysis

Analyze hydrogen bonds made in a trajectory.

1) Open trajectory file into a system PDB file

2) Analyze hydrogen bonds

Find lipid bilayer thickness

1) Get the lipid bilayer thickness for each frame

2) Get the average thickness in the trajectory

awk '{ sum += $2; n++ } END { if (n > 0) print sum / n; }' thickness.txt