Hi everyone, I have a pdb file which is a trajectory of one protein. How can I use VMD to classify the frame of the protein according to the conformation and draw several images which image contains the similar conformation of the protein? I would really appreciate if you can help me or provide any suggestions.
The example of the image which contains the similar conformation of the protein in shown below.
VMD used to have a plugin named "Clustering Tool" to visualize clusters of conformations of a structure, But it seems that it is down now.
Gromacs had the same but they said the algorithm is wrong.
I can recommend BitClust which is fast and easy, and the author is really kind and friendly :) you can ask if you have any questions. All these are based on RMSD value and using the same algorithm.
you can also use Bio3D (http://thegrantlab.org/bio3d/index.php) which cluster conformations *you can use the website or the code* but I am not sure if it is free, there is a tutorial on JOVE. good luck
VMD used to have a plugin named "Clustering Tool" to visualize clusters of conformations of a structure, But it seems that it is down now.
Gromacs had the same but they said the algorithm is wrong.
I can recommend BitClust which is fast and easy, and the author is really kind and friendly :) you can ask if you have any questions. All these are based on RMSD value and using the same algorithm.
you can also use Bio3D (http://thegrantlab.org/bio3d/index.php) which cluster conformations *you can use the website or the code* but I am not sure if it is free, there is a tutorial on JOVE. good luck
You can use tools which can be found in analysis of VMD. These tools can calculate dihedrals phi and psi as well as secondary structures over the simulation time. However, I suggest you to keep only peptide in your trajectory (convert it) and slice the trajectory on smaller parts since VMD has a limited memory. I would suggest you to run over the xtc-format of the trajectory. Result is well-visualized by VMD, but I would advice you to write own code to plot changes in secondary structures in a more convenient way. You may check my latest papers and Supporting Information for that.
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