Very helpful. Thank you!

Nice video. I have a question. How can we know which features turn ON and turn OFF?

Do we need to do protein preparation steps such as adding hydrogen and energy minimization on our protein structure before that?

THANKS!

Where to find moe for free please.

Thank you sir 😁 No wonder my results got overlapped after docking with vina when I straight open in BIOVIA

en mi programa no me da diferentes conformeros solo uno ayuda

good way to understand the method

Thank you so much

Thanks for your insightful sharing. I commented yesterday but somehow the comment is missing. I have installed academic desmond successfully followed your former video. But my molecular dynamic job launch failed and got error like “cuda driver version is insufficient for CUDA runtime version”. But this configure worked fine when our schrodinger license are not expired and other gpu-accelerated job works fine(not schrodinger or desmond). When the schrodinger license is available, got same error, the support team suggested running "licadmin INSTALL -c 27008@mu01" on gpu01 and problem solved. But I am confused wish academic desmond. Maybe there is something wrong with my configration rather than cuda driver and cuda toolkit. Could you please have a look and give me some advice if you can? Thank you！

Really thank you so much brother 2 week search my qst ans finally am got your video

Please i need download software

"ExecutiveAlign: mobile selection must deruve from one object only" I exactly follow the steps, but still got this error..cant calculate rmsd..can u help me out pls? same issue i got . please answer to this

Thank you so much for sharing your knowledge with the world n yeah it helped me alot... btw i can sense that you are a kashmiri😊...keep it up

Hello every one moe docking give multiple pictures for the same amino acid with same number of residue in peptide when checked ligand interactions, Is that normal or error occure ,cause??

How can I make energy minimisation for ligand

how to make the PDB file?

thanks!

Is energy minimization for protien essential if I achieved correction and prolongation step ?

Hi sir so grateful for you can I get an analysis result such as rmsf and rmsd by this software

Thanks for the useful video. As far as I see, you are doing system preparation and MD simulation using the Windows operating system. Maestro is ok but I know Desmond works under Linux. How did you perform MD simulation with Desmond under Windows operating system? Thanks

Thank you sir for this tutorial. I had two queries. Is the software free ? And how long it will take to complete this simulation for 20 ns simulation time?

For my protein i can't able to find hydrogen interactions in pymol. even after docking in pyrx .how can i get hydrogen bonds and interactions

Very well explained.

Eres un grande maquina , gracias de todo corazon :)

Ubuntu is not working on my PC. What should I do?

Thank you. My labtop windows 10 but i cant open autodock after download it.

Very helpful video. I seen in your console box, when you were giving a command that your directory is saved as "COMSATS". I am also a student of COMSATS university. And I am doing computational chemistry with blind of machine learning in my MS research. It is a great pleasure to see someone from my background to helping out people with this dense topic. Really proud of you bro/sis.

Only available for NVIDIA GPUs? Any idea how to set it on AMD GPUs? Thank you

Es ko kiss software pa banana h plz bta skty hn ?

This was amazing, thankyou so much sir.....

Thank you so much, I have installed GROMACS for my vmw.

Thanks for the wonderful video. I've done docking for a series of GPCR with their native ligands using MOE. Unfortunately, the obtained affinity and rmsd aee not reproducible. I did as below: First I downloaded a pdb file. Removed all unwanted compounds and water molecules. In presence of the native ligand I did a quickprep. Finally docking (by default parameters). Could you please help me with my problem? By the way I saw in some video, some people do minimization before quickprep. Do you suggest it?

how to install wifislax x64 3.3??

How do I fill the registration form

I am getting, command not found. please what should I do?

I don't get grid box outcome file... It shows an error as to provide receptor

Hi, I have a question. If l don't have any gpu can I run a simulation?

I like the music you put over the video. It really helps me not be so frustrated.

When I click for 2D diagram "Ligand is not single fragment." This pop-up appears... What should I do?

How to Em 1000 compound at same time

Hello sir could you explain why you used B9990001 folder instead of the other 2 models generated?

Thank you. It works. PS 1. looks like NAMD works better with VMD 1.9.2 than version 1.9.3 PS 2. You can delete the VMD and NAMD folders after installation PS 3. If you need to delete VMD -> sudo rm /usr/local/bin/vmd && sudo rm -rf /usr/local/vmd/ PS 4. If you want to delete NAMD -> sudo rm /usr/local/bin/namd2

Non si capisce un cazzo

We're to find gromax file

We're can I find the gromax file

Is this md simulation?

I tried installing Desmond 2018.4 but then the alldocs product isn’t compatible. How do I fix this please

THANKS

Thanks alot for this tutorial. I could fill the missing amino acids but after performing docking I realized that the amino acids position have changed.