RMSD analysis of trajectory (DCD file) using VMD
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- เผยแพร่เมื่อ 11 ก.ย. 2024
- This video shows you how to calculate the RMSD analysis of aa protein using the software VMD from the University of Illinois (www.ks.uiuc.edu/).
VMD is a powerful tool for analysis of structures and trajectories. Numerous tools for analysis are available under the VMD Main menu item Extensions $
ightarrow $ Analysis. In addition to these built-in tools, VMD users often use custom-written scripts to analyze desired properties of the simulated systems. VMD Tcl scripting capabilities are very extensive, and provide boundless opportunities for analysis.
Example of a built-in analysis tool: the RMSD Trajectory Tool
The built-in analysis tools in VMD are available under the menu item Extensions $
ightarrow $ Analysis. These tools each features a GUI window that allow one to enter parameters and customize the quantities analyzed. In addition, all tools can be invoked in a scripting mode, using the TkConsole window. We will learn how to work with one of the most frequently used tools, the RMSD Trajectory Tool.
thank you sir, I think your video is helpfully. i will calculate a radius of gyration and I bit confused about its step . hope you can build a video how to calculate it. jazakallah
The next one will be about Rg calculation , stay tuned !
Hi Dear, I have been working on modeling, let me keep it short I have done 2D and 3D molding of the concerned protein and ligand by using Discovery Studio and Auto dock Vina and further want to plot an RMSD graph, but I have no idea how to proceed my work, I had watched a lot of videos and read many articles but I have no clue from where I have to start plotting the RMSD value, even I have RMSD l.B and RMSD u.b values. I would appreciate your time.
same problem ...i need to plot RMSD GRAPHS.. but no source
if you find any solution plz tag me
Could you find any solution to it sir?
Good explanation
Thanks!
tübitak ?
Hello, is this code in the video for calculating RMSD of the protein's backbone? if not, how can I calculate RMSD particularly for backbone?
Hi, but in x axis in vmd we are getting frame, how to get time in x axis
First, thanks a lot for giving such informative videos. Is there any video for steered molecular dynamics(SMD) using quick MD?
should we need to load ref molecule as well? what kind of ref molecule if we want to calculate RMSD of protein and complex
Does VMD takes the protein in pdb or pdbqt format
Thanks for this useful video. Could you explain how to plot Total energy, potential energy vs Time too? How to change x-axis to TIME?
Hi, you are welcome. I will try to post that soon but as a quick solution you may need to export your data as a txt file then plot it with tool available. Don't forget to hit subscribe , we are close to 600 geeks learning together :)
Hi Muhammad, can you pls make how to easily use BFEE with minimal cmd use and in a user-friendly way? Thank you for your efforts. Much love.
Thanks for such an informative video!! Could you also explain how to calculate rmsd between atoms of two molecules?
How to combine rmsd plots of two different simulation runs?!
hi mohamed why that in vmd x axis is a frame, and i see in other picture there were time (ns) in x axis, is it actually same ?
No it is not the same. VMD deals only with frames. Since VMD doesn't know your time step it can' t calculate the corresponding time. You should do this by your self based on your time step say it is 2 fs/step then each frame is corresponds to 2 fs and so on
Thanks for sharing! I have a little question about how come your VMD could determine file type automatically? Mine need to select manually every time.
Hi, It should does actually. You may try to uninstall and install it again or install the latest version also don't forget to run it as administrator
@@Mohamedshehata Thanks for your help
Dumb question, but are the values for RMSD given by NAMD in Angstroms or nanometers?
Hi Tyler, VMD calculates RMSD in Angstroms
@Tyler Maxwell save the data as a txt file and plot it with any scale you want by using any plotting tools
hello dear Shehata,
I'm getting error says that permission is denied, when I save the trajrmsd.dat file of trajectory in vmd. could you please help me how to fix this issue?
Run VMD as SUDO or administrator
@@Mohamedshehata
many thanks
it worked
I am trying to calculate rmsd of each frame a trajectory from molecular docking results. I loaded the trajectory and my reference complexe, but i am not getting align typing the backbone of the receptors in the selection atom box. The receptor of my reference complexe is the chain A and the receptor of the resoults is the chain X. How can I type correcttly to align both receptors? I cant find a good tutorial that explain better about typing in the selection atom box. I still dont understand how its work at all.
Hi, I did not get you totally, in order to calculate the RMSD you need to load your psf and trajectory then align your trajectory to the first frame no need to load the pdb. For the selection box , you can write protein or chain A or resid 100 to 200 for example .. hope this helps
@@Mohamedshehata, thanks for the answer!
In fact, my files are .pdb and the ligand of my receptor are a peptide. When i type protein or chain A, for example, generates an error message about no atoms selected or something about difference in the number of atoms.
@@rayzaadriellealmeida2321 I think I should have the files to solve the problems but you said at the beginning that you want to calculate the rmsf for each fram and this means that you have a dcd file not a pdb.
you can send me an email with better explanation along with your pdbs and I will try to figure it out
@@Mohamedshehata excuse me what should i write in the selected atoms if I want to calculate RMSD for docked complex (protein+ ligand)? should I write resid and choose the range in which my ligand binds to the protein? or write all or protein or what? could you help please?
Thank you for this video, would you please explain how to calculate RMSF
it is in my channel , watch it !
here it is th-cam.com/video/CkCREhk1SL4/w-d-xo.html
Thanks for the video,
Can you please explain how to save trajectory snapshots (frames) in pdb format after aligning with reference frame?
Yes, sure
I have done NVT simulation for 50000 steps and generated a nvt.dcd file Now I want to plot a graph RMSD verses pikosecond. As per tutorial I made rmsd.tcl file but I couldn't get RMSD verses time plot it gave me rmsd verses frame plot it showed 500 frame. Please help if you can
If you know the simulation time step you can easily the picoseconds corresponding to your 500 frames
@@Mohamedshehata Please elaborate, I have 2 fs/step with same information as the question
Hi, I saw how you loaded dcd and psf file in Vmd. ..But my files are not behaving as it should be. My question is how to create psf and dcd file from pdb for rmsd trajectory ..Thank you...
kindly check the other videos about molecular dynamics simulations in my channel .. good luck
Can you please share link..Thank you.
@@sohaibroomi8329 I said you can go to my channel and check them
@@Mohamedshehata With due respectfully Sir, I didn't find with title or caption. Should I go through your videos one by one.??
th-cam.com/video/hN1BiiT-ECo/w-d-xo.html
Hi
Thank you for your great video, but I have a question about how can I calculate the RMSD of a big dcd file using bigdcd.tcl script?
Hi you are welcome, how big is you dcd , frame number ?
@@Mohamedshehata I did simulation for 0.5 ns and I got (24 Gb ) (10,020 Frames) but now I have to do about 100 ns simulation
@@solasola2897 I have not used it before but , are you sure that you need this number of frames ? too much . I think VMD will crash even if did not I think that going into every single frame is not right idea
how to get the x axis in ns ?
I already answered this question ...again if you know the total number of steps and you integration time you can easily get it
how analyze data from gromacs using vmd
Dear Geordano Palacios, the point is that VMD want only frames to start the analysis but loading the gromacs output is different , you may watch this video to know how to load a gromacs trajectory to VMD, kindly let me know if it worked with you ..best
th-cam.com/video/PlPYc4jMA4c/w-d-xo.html