I have run a 10ns molecukar dynamic simulation and now want to superimpose my protein at different nanosecond range so that i can compare my ligand moment. Pls suggest me a way to align all proteins from different frames into single backboned structure. Suggest me a way in vmd software preferrably. Any software is ok unless the compelte procedure to do it is provided..thanks in advance
Tje RMSDTT plugin in VMD can do the alignment of the entire trajectory easily: see http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/ (you ca obviously select the backbone or anything else you want to align to). See also this tutorial: http://www.ks.uiuc.edu/Training/Tutorials/vmd/tutorial-html/node7.html
As Bartosz Trzaskowski suggested, is indeed nice.
You can also try like this.
Load the structures in VMD and go Extensions--------->Analysis---------> RMSD calculator -----------> type residue range (It must be same) and click on align. (This will superimpose all the structures and click rmsd to get value.)
Meanwhile you can change color-id to differentiate the structures by going representations menu.
Good luck
I like UCSF chimera cluster analysis (Very powerful).
http://compbio.biosci.uq.edu.au/mediawiki/upload/6/6a/Clustering_molecular_dynamics_trajectories-_I._Characterizing_the_performance_of_different_clustering_algorithms.pdf
http://www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/ensemblecluster/ensemblecluster.html
Navneet chaturvedi...vmd throws an error "measurefit : selections mucy have the same number of atoms" can u tell the solution in little detail pls..
please find visualization state of VMD. and do like this
1. Open VMD
2. Go Load visualization state
3. Go to Extention------> RMSD calculator (make range 5 to 585)
4. click on align (it will show you superimposition)
5. Now click RMSD to get rmsd
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