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You didnt show your results of 3d structure

Dear Dr you shared a very valuable tool to do simulation but could you please let me know why some commands are not working should we buy access of LGPU or what ?

sir number to dain apna

Hi sir .. thank you for the helpful description... can you please help to perform docking of ligands-metalloprotein (protein with metal ions as co-factors in receptor) using autodock?

Muchas gracias señor, que dios se lo multiplique

Hello Dr. Rehman, Thanks for the insightful video. Please I am Mohammed from Ghana. I am using AutoDock Tools, AutoDock Vina and DS visualizer. When I do the docking, the ligand breaks at the rotatable bonds of the ligand. This makes it difficult for me to calculate RMSD and only one section of the ligand shows in the 2D diagram viewed by 2D visualizer. Please is there anything I am missing. Thank you.

Sir that's amazing pls can we do that on laptop CPU system?

Thanks a loooooot

Sir can u please mention the name of protein similarity check software plzzzzzz

Sir, Is it possible to dock even after the ligand size is more than 15kb?

Hello sir How i can docked of coordination complex with protein

Hello sir How i can docked of coordination complex with protein

Hello sir How i can docked of coordination complex with protein

Thank you Dr Muzammel Rahman for the comprehensive tutorial on MD using GROMACS. I have gone through the tutorial till the end and it was very helpful, indeed. One thing I noticed at the end is, that you forgot to combine the two commands together i.e., printf "proteins" | gmx xxxx x x x x x x xx x x xxx.. You just forgot to add " | " to your code. If you had added this the code would have worked correctly. Anyhow, the session was nice and I understood many things from this tutorial. Great work.

how to fix swig/python detected a memory leak of type 'BHtree *', no destructor found......in autodockvina ...thanks a lot

in my case xmgrace command is not workingg

Sir you are using Mac system but how to do on window 10 plz both alpha fold2 and RoseTTAFold?

What's the importance or Idea from of this md simulation of ligand without protein ? !! Thank you sir for your effort !!

sir i want guidance regarding my research work on protein prediction how can i contact you

very informative. I predicted 3D protein structure using Phyre2, then got a model with 99% confidence, and 18 % coverage. 58 % of residues are disordered. May I use this protein for docking analysis?

Hi sir, after prediction, I got JSON file and CIF file. Would you kindly inform how to convert this file as pdb format? Thank you.

please you have not shown how to dock protein-peptide, just how to upload because the peptide is not in pdb?

how to dock 200 peptides at the same time with a receptor protein using auto dock vina

Thank you so much. Can I dock if my ligand is outside protein?

Im performing docking on a known active site so i limited the gridbox around the active site only. Some of the conformations i got after docking were outside the grid box. Is that normal?

Sir can you tell me how to dock protein protein and peptide

Sir can you help me how to find the binding of peptide in between two protein protein interactions

Thank you so much dear Rehman

Tanks to you Sir, this is a great video

Hello professor , thank you so much for you explanation, i wanna ask you if the pdb file of the complexe generated with cb dock can be submitted to MD simulation without any problems?

Greeting will this command works for gromacs 2024.1 and the new cmake 3.28.4?

sir also make tutorial for protein ligand complex simulation of uploaded protein complex own

For the CB dock, it is necessary to perform energy minimization for ligand molecules before uploading the file.

How to do md simulations for 20 nsec and how to obtain the graphs ?

How to do md simulations for 20 nsec and how to obtain the graphs ?

bhai 1KAI k ilawa bhi koi use kr lo..... local files k sath kese kr skte wo bhi bta do

thank you so much

Assalamu alaykum Sir. Can I perform MD simulations of two organic molecules (including any solvent) using Chimera?

Sir how can we know which ligand should we use?

Assalam o Alaikum sr g ap k student hb hum apk prhny ka triqa bht bht acga h

How many ligands can be docked in cb dock?

May I know the protein for finding antianginal activity pls help sir

assalamu alikum sir, i got called processerror when installing gromac . what do i do.

Sir can we do just protein structure prediction as thesis for project?

Hi,doctor such a great lecture 👌 with fantastic explanation and exclusive work work. Allaha bless you Wishing you sucess and cooprate with you in work❤🎉🎉🎉😊

please change the title, there is information regarding machine learning

sir how long GROMACS can be run in colab ? what is maximum ns can be run ?

Thank U Dr. Muzammel Rahman..

Assalamualaikum Dr. Muzammel Rahman...I am Frengki from Indonesia..thanks alot on all your dedication for upload this video

What you are explaining is what we can see on the screen. We expect scientific explanations for God’s sake