Thank You So Much!!!

Thanks a lot.. This was very helpful 😄

I want to know about ligand ligand docking

Good day Dr. I want to ask if multiple ligand can interact with receptor in autodock 4?

please make a video to implement hse06. Also please let me know whether HONPAS is compatible to siesta 4.1 b4 or not.

Thanks. ☘

How to implement hse06 here?

Would it be possible to show a tutorial on how to make heatmap or UMAP/TSNE using the data? That would be very helpful

So diff dock can achieve by Python shell script or by gui of nvidia ? and same result ?

What is the difference between rmsd of ligand with and without h heavy atom ?

Hello Sir I want to ask that in papers the values are written as for example: -7.8 ± 2.3 , so I would like to know that how can we write the values from the results like this? Do we use SD or SEM? and there are two columns of each so which values we should use. Kindly help me

I have a huge interest in structural bioinformatics and i am planning to pursue a PhD in this field along with generative drug design. this channel is very helpful and i came across all of your videos, very useful resources. please post regularly so that a beginner can learn from a pro in this field. thank you!

Hello, how can I save the flowset with the cells that are only includes in the gates?

What if i use two types of atoms and use hybrid functional for both, how to define the species then?

I don't think there is a parameter called --log in autodockvina, when i ran this sh script it showed "Command line parse error: unrecognised option '--log' ". I use autodock vina version 1.2.5

thank you which mac processor you are using ? Is it M2 or other M series or intel versions? I am trying to create the environment but it is not working !

Very clear and well understood explanation. How to run simulation with 10 chunks for 100ns simulation. Please make a video or guide me. I tried it for several days but coudn't get over the line.😢

Thank you for the video. I have a question if i run a 100 ns simulation but i want to calculate only the last 10 ns, what is the startframe and endframe should i use?

How to make size x y z .. is it standard value

Nice presentation! These days, only programs that harness the powerful GPU could be popular since over 98% of world compute power comes from GPU in the current days. Could you introduce another one with use of GPU?

Thanks 🙏 you are the best 🎉 I have a problem.. after docking the ligand was fragmented.. what I have to do

thank you for great work, I notice from your result Gibbes energy landscape start from 0 Kj/mol. and I try to do that I get the same ,why we didn't get negative value even MMPBSA is = -9 kcal/mol

Thank you very much for this session sir. However, i would like to ask, is it possible to use files (xtc, tpr , ndx) generated from version 2024 of gromacs in this MMPBSA analysis?

Good afternoon, I enter the mgltools page but I do not get the download links, is there any alternative to download it? I don't know if they have been removed or it's my problem. Thanks

Thank you so much for the video. One question, blind docking can be used also to see covalent interactions between a ligand and a protein ?.

Sir, CGenFF server is no longer freely available . I recommend ATB, Acpype or such kind of other servers.

Thank you so much for your great teaching. It is very helpful for me.

Hi Sir, Your videos are very useful and engaging. However, using the mdp file from OPLS to simulate a protein in water with the CHARMM36 force field seems inappropriate, as the OPLS mdp file lacks parameters for the CHARMM36 force field. Below are the missing parameters: constraints = h-bonds cutoff-scheme = Verlet vdwtype = cutoff vdw-modifier = force-switch rlist = 1.2 rvdw = 1.2 rvdw-switch = 1.0 coulombtype = PME rcoulomb = 1.2 DispCorr = no

Thank you very much for sharing your knowledge on siesta! In this tutorial you mentioned that other than the molecule (NO2) you could also put other molecules or even DNA. How do you put DNA? What would that be as a representation and how would you do that? Thank you very much!!

Sometimes the automation is stopped due to maxwarn warning. How can i resume the automation?

I want to know how you install windows on mac book and use both side by side

Hello Pritam in my case sh script.sh command not working. IT show bad for loop variable. Please help

I've been using the old Avogadro version for a while, according to the one you're using, and I've been encountering too many mistakes. So I need a new version of Avogadro; could you help me find the download file?

Hello Pritam, Introducing Nvidia's DiffDock, which uses generative AI for the docking of small molecules is indeed a promising idea. However, there are some inaccuracies in your video that should be addressed. It's important to ensure the information shared is scientifically sound, as misleading content can misinform viewers who may trust your statements. Specifically, there are two points of concern regarding your docking of remdesivir into the structure of SARS-CoV-2 Mpro: (i) Remdesivir is not a substrate of Mpro. (ii) The form of remdesivir you docked is not its active form. It is a prodrug form that requires metabolic conversion to a form that is accepted as a substrate by the target enzyme. I recommend reviewing these aspects and conducting further research to ensure accuracy in future content. It's essential to have a solid understanding of the science behind such AI techniques to maximize the potential of tools like Nvidia DiffDock and ensure their effective use. Otherwise, these AI tools can also be considered useless! Thank you - Kamal

How necessary do you think a Ph.D. is in the US? Or do you think a master's is sufficient?

Dear Why you are not describe how to make .mpr file?

I noticed that you have linux system but you are using windows version of swiss PDB viewer Why not not using Linux version? Excuse me sir but I have same issue

Its really cool. Thanks

When I try to open the pdbqt file of ligand conformations using Discovery Studio, the conformations of the ligand are looking destroyed. So, the main chain of the ligand is not looking truly. As if molecule is containing Siyano, etc. groups. I just prepared the ligand using Autodock 4. The same problem is popping up again. Whenever I want to save my ligand as pdbqt, Discovery Studio is showing a destroyed structure, not the real molecule structure. I've done what you've done. If I write as complex, I can see the ligand structure as it should be.

Normally, dock.dpf file containing AD4.1_bound.dat isn't running because the program can't find AD4.1_bound.dat file. When I encountered this problem, I looked at your dpf file and saw outlev 1 instead of AD4.1_bound.dat. Then I changed as outlev 1. Now it's running without any mistake, but according to what I've read, outlev just ignore the mistake. I'm looking forward to hearing from you. 🤔

Sir if I want to change the simulation run time length, do I change the steps only in the mp.mdp file or other mdp files too?

Is this for just single molecule docking or it can do virtual screening?

Thanks, your channel is very useful !

IF I want hydrogen bond occupancy percentage for one residue during the simulation what cod should I use, Thank you.

Hi, I have some questions. I finished docking and opened the results. but, my results have 23. The only top 10 results are not showing

Another masterpiece of work from you. We are learning a lot from you. Sir one request if possible can you upload video on 3D graph of PCA analysis. Further if possible can we correlate the Gibbs free energy with the RMSD. Thanks for wonderful work❤

Thank you sooo much for the video. This is really helpful for me! I followed through the tutorial and obtained my analysis results, but I'm having a bit difficulty understanding the plots. Could you make another one on explaining how to read them?

What is liked in this video is "Correcting the Errors". Like you really understood the errors and then solved them. Now, I will be doing MD simulation for my protein-ligand complex. Subscribed

Do have any of your videos with docking validation and statistical analysis? If possible I would recommend to do that

Hi, Can we extract the most stable comformation from FEL?