EP 11 | Post MD Simulation movie for visualization Protein-Ligand complex trajectories | Gromacs
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- เผยแพร่เมื่อ 20 ส.ค. 2024
- Hi,
I am Dr. Dweipayan Goswami,
Welcome to my TH-cam channel "Learn at ease"
In this video I have explained how to perform post MD simulation visualization of Protein-Ligand Complex in the from of Video and how to export the video.
Tutorial, Codes and Files used in this video will be found at Github :
github.com/Dwe...
This video is in continuation with my previous video:
EP 10 | A to Z of Protein-Ligand MD Simulation in Gromacs | Reusable commands and files provided
• EP 10 | Protein-Ligand...
The files of protein ligand complex is the docked complex which I had prepared in my video :
EP 1 | MOLECULAR DOCKING in UCSF CHIMERA by VINA Plugin from Scratch in Linux
• EP 1 | MOLECULAR DOCKI...
Other important videos available in the Playlist :
• Bioinformatics-Unplugged
One of my teachers used to say, "If someone chooses the hard way to teach you something, know that he doesn't know anything." I haven't seen anyone teach better than you on the TH-cam platform. For this reason, thank you endless thanks.
Thank you for the support and acknowledging my work
Thank you for your wonderful explanation, it helped me tremendously😁
Learn to ease, ths name is perfect for your channel
Thank you very much...
Really you did a fantastic explanation and work. Thank you,sir.
Sir can u make a video on mmpbsa. Thank you so much sir for this md videos. It is very much useful
Thank you sir for the valuable tutorial
Thank you very much
Keep uploading
One of best and easiest way to perform MD simulation, thanks for making so east and conceptual detailed video .
I have a question.
That if a drug has mechanism of doing conformation change in protein or denature it so how it can be checked through MD simulation or RMSD or protein stability value kindly elobrate it
Thank you so much sir
😊
sir i could not find the MD /ensembled analysis in my tools of chimeraX. please response how i can get that and also is it necessary to have gromacs and chimera in the same system to get that. please reply
Nice explanation, however, I find that in a lot of tutorials, waters are stretched, the protein is rotating around, does not seem correct, did you treat the PBC (trjconv) and remove rotation and translation because then only a correct trajectory can be visualized. If you calculate RMSD to first frame within this trajectory, it is going to give weird results since you didn't remove rotation and translation.
Agree 💯
Sir, I have performed a 50ns md simulation, can I extend the simulation to 100ns, if so please guide me
thank you.
Can you please provide all the output files, please
Hi! sir! if I have more than one protein-ligand complex pose, there should be different runs per pose?
Yes !!