Great work👌. Needed GROMACS protein- ligand simulation, umbrella sampling and MNGBSA/MMPBSA. Sorry for becoming greedy, your work made me greedy. Thank you
Thank you for your kind help and tutorial for others. I have a query in this regard. Could you please tell me how can I determine the RMSD value between the protein and ligand in this case. It will be a great help for me. I will highly appreciate your instructions.
@Muniba Faiza Thank you for your reply. Yes RMSD value is given in the log file from Vina. But I wanted to know about its manual determination. Later, I have found that it can be calculated using PyMOL wizard > measurement option. Thanks.
This is so useful thank you! I have one question( I am a student). How do you see the polar interactions in PyMol in a protein-protein complex? We wanted to edit those interactions to make the complex stronger but we don´t really know how to do it.
Thank you What are the pymol commands to automate the process: show ligand pocket show interactions show residues label residues make high quality figure
sir i have Some questions please answer them if you can... I have windows OS and want to dock multiple (600) newly designed Ligands with my targeted protein. so my questions are.. 1. do i have to dock them one by one..? (obviously it will take so much time to repeat the steps) 2. can I just dock all of them together.? and if yes how? And is it possible in windows or i have to use Linux? (actually i mean to just put all of them in a line so that they can get docked one after other) (my problem is that i have seen someone who docked more then 100 Ligands. what he do in actual is that he gave a command and system kept running for 1 whole day for docking studies. he used Linux OS and this is my concern that can i do it in windows OS too..? )
Thank you for the informative video! Question: When I loaded my ligand, it was not within the protein but was far out of reach from the protein. Is this a good thing?
You are awesome. There are few smart humans that will watch the video, hence few views. But this is treasure!
Great work👌. Needed GROMACS protein- ligand simulation, umbrella sampling and MNGBSA/MMPBSA. Sorry for becoming greedy, your work made me greedy.
Thank you
Fantastic explanation of how to analyze the complex.pdb file generated into the autodock vina.
This video clear my much more doubts... Thank you mam
Superb explanation
Thank you! :)
Wow Mam you explain it awesome
Hello. Thanks for the video. I have a question, what´s the difference between the options cavities and pockets only and cavities and pockets (culled)?
Nicely explained. Could you please explain how we can determine amino acids residues of binding cavity around the ligands?
Hello, im having some difficulties selecting atoms. Can you please tell how to select them
You are my lifesaver. THANK YOU
Incredible! Thanks a lot.
Thank you for your kind help and tutorial for others. I have a query in this regard. Could you please tell me how can I determine the RMSD value between the protein and ligand in this case. It will be a great help for me. I will highly appreciate your instructions.
@Muniba Faiza Thank you for your reply. Yes RMSD value is given in the log file from Vina. But I wanted to know about its manual determination. Later, I have found that it can be calculated using PyMOL wizard > measurement option. Thanks.
Great wrk dear and thankyou so muvh
This is so useful thank you! I have one question( I am a student). How do you see the polar interactions in PyMol in a protein-protein complex? We wanted to edit those interactions to make the complex stronger but we don´t really know how to do it.
Mam what should be the minimum activation energy for suitable docking complex..??
Thank you
What are the pymol commands to automate the process:
show ligand pocket
show interactions
show residues
label residues
make high quality figure
Is there any way or software to analyze protein-protein docking results. Kindly guide...?
How to label the specific amino acids that are interacting with ligand?
Thank you so much for the tutorial. 👏👏
great work guys! its really informative and helpful! :)
I wish you could tell everything in detail like what rmsd is and everything.
When i try to preset the ligand sites, no polar bonds were shown. Did i do it wrong?
How to save pdb file of a single pose? Please reply
sir i have Some questions please answer them if you can... I have windows OS and want to dock multiple (600) newly designed Ligands with my targeted protein. so my questions are..
1. do i have to dock them one by one..? (obviously it will take so much time to repeat the steps)
2. can I just dock all of them together.? and if yes how? And is it possible in windows or i have to use Linux? (actually i mean to just put all of them in a line so that they can get docked one after other)
(my problem is that i have seen someone who docked more then 100 Ligands. what he do in actual is that he gave a command and system kept running for 1 whole day for docking studies. he used Linux OS and this is my concern that can i do it in windows OS too..? )
thanks allot, i will share this
How did you get binding affinity at 3:40? Confused on how to obtain that
Is it ok to take pdbqt file of receptor?
My ligands did not bind at all the active site. I don't no Y
differencce between chimera and mgl tools?
Thank you for the informative video! Question: When I loaded my ligand, it was not within the protein but was far out of reach from the protein. Is this a good thing?
@Muniba Faiza Thank You!
Sir my ligand is also far but when i m add in autodock the ligand binding is shown easily means am i correct
Mam how to know the information to publish the paper
how to convert cif fill to PDBQT Fill
How to choose other models
Can I download this video for study in China?
After knowing the different binding conformations what can we do next