Best tutorial for introduction to molecular dynamics thanks alot. Please after performing molecular dynamics with Autodock vina how do you prepare topological file of your protein complex with amber. One of the main issues with Amber is recognition of the non standard residues which are usually the ligand. Is there another méthod apart from the resp procedure for ligand recognition by Amber software? Thanks
Great webinar Girinath ji. I am new to this field basically motivated by understanding the bio-sensor design field. What simulation solution would work for studying the MD of proteins in vivo and their interaction with electromagnetic fields in various spectra from RF to NIR/IR and Visible light.
I want to perform differentially gene expression analysis from GEO data set. I want to know, can i able to perform two data set with two different packages .For example i want to analyze one data set by limma and the other by DEseq2. So i want to know is it valid to analyze with two different packages?
Certain changes in complexes takes place only after certain time as I have discussed in one of the slide. How much time required for specific calculations or objectives.
Sir I want to understand the unbinding dynamics of dynein motor and tubulin, so should I use a coarse grain model followed by smd? What should be the best force field to do the same?
Great session. Really helpful for a beginner in MDS. Thank you.
Best tutorial for introduction to molecular dynamics thanks alot. Please after performing molecular dynamics with Autodock vina how do you prepare topological file of your protein complex with amber. One of the main issues with Amber is recognition of the non standard residues which are usually the ligand. Is there another méthod apart from the resp procedure for ligand recognition by Amber software? Thanks
Sir what are the basic minimum system requirements for GROMACS software in linux system
9:09 enjoy
Great webinar Girinath ji. I am new to this field basically motivated by understanding the bio-sensor design field. What simulation solution would work for studying the MD of proteins in vivo and their interaction with electromagnetic fields in various spectra from RF to NIR/IR and Visible light.
Can someone tell me what program can generate the picture at 52:50
PLIP, LIGPLOT+, Discovery Studio etc.
How to perform hydrogen bonding analysis using molecular Dynamics
Will u please that protein modelling
We already have posted the tutorial on protein modelling using MODELLER
th-cam.com/video/nFCKeGa73gc/w-d-xo.html
Sir, Could you please any videos based on carbohydrate simulation?
Yes in my todo list, it will take some time.
I want to perform differentially gene expression analysis from GEO data set. I want to know, can i able to perform two data set with two different packages .For example i want to analyze one data set by limma and the other by DEseq2. So i want to know is it valid to analyze with two different packages?
That is extremely useful thank you.
You're welcome! Thanks for watching and looking forward to your feedback.
Your a good proff
Sir, in protein-ligand MD. if the ligand is bound with protein like for 200 ps then why we do a simulation of 100 ns? and what we check?
Certain changes in complexes takes place only after certain time as I have discussed in one of the slide. How much time required for specific calculations or objectives.
Sir can u please kindly explain how to identify the domain in protein structure ... and how to really know whether the simulation has worked??
Sir I want to understand the unbinding dynamics of dynein motor and tubulin, so should I use a coarse grain model followed by smd? What should be the best force field to do the same?
@Girinath pillai Sir..Can we have a detailed demo on how to perform Molecular Dynamics Simulations
When will be the real live session of practical?
If we do not solvate a system what kind of artifact it will provide?
Skip to 9:00
Thank you Sir
Thank you much, Your teaching is superb. Please, sir, can you make a video on how to install cafe1.0 for windows 10.
Thank you so much sir for the video.
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wrong info