hello, i find molecular dynamics hard to learn as i had no prior experience with coding and linux (what my teacher recommended me to use), videos like this makes it very easy for me to understand the concept and how to do it. THANK YOU FOR THE VIDEO!
Sir, at 9:25 you add Kollman charges to the protein. However, at 15:23, when you load the protein macromolecule, you click on 'no' for preserving Kollman charges. The next popup box states that Gasteiger charges were added. So, should we add Gasteiger charges for the protein?
At 17:55, Spacing parameter is set 0.375 A, but this is not used by AutoDock VINA. Changing this parameter affects the grid box size. So even you attempt to perform site specific docking, the docking is going to be blind docking due to this parameter. I am not able to get the clarification about this parameter while docking except VINA official tutorial has this option set as 1.
Great tutirial and very informative one. Kindly if possible add ligand and DNA docking tutotrial. Sir it would be great job on your part. Thanks regards
Thank you Sanket Bapat. Both the videos are very neatly and clearly presented. Highly informative. But once after docking how are we to interpret it in the paper. Any suggestions or advice regarding the same.
Hi thanks for this, came at the right time! When adding the grid box, is it generated automatically at the binding pocket or will have to adjust it? if so, how do i ensure its the 'correct' coordinates?
Thank you sir for such a nice video. One question- if we don't know the active site, why we are not enclosing the whole protein inside the grid by changing dimensions.?
Could you make a video showing how to dock in Vina Auto-docking using some flexible active site waste? I need my molecule to interact with specific residues and I don't know how to do it. Please.
Hi joyce I think you cover all the protein by doin grid box so it will be flexible as you took all protein whereever will get less energy it will enter
As we all know that docking simply interaction between receptor and ligand molecule, before docking we do remove the water molecule and some other additional ligands molecule , and add polar hydrogen bond also, Afer that we dock between receptor and ligand molecules, and more negative sign give the good stability.....but sir my question is that in natural condition how water and additional ligands remove from receptor molecules and how will i add polar hydrogen also?
Good day to you sir. Thank you for this excellent interactive session. I have a query, What is to be done if ligand profiles are not seen in the downloaded material from PDB.
Hi very informative tutorial on AutoDock Vina but I have a question which is that what about if we don't know about the ligand binding site of our protein so how can we set the grid?
Should we follow the default grid box dimensions mentioned in the autodock vina ? Wouldn't it be correct if we first checked literature for the docking site and then changed the dimensions of the grid box? Dr. Sanket , could you clarify this ?
Hi Dr. Sanket. I am an IBDP 2 student. For my school project I need to conduct multiple ligand simultaneous docking. I was able to conduct single ligand docking but am unable to understand how to do MLSD. Can you please help with instructions on how to do this. Thank you
I have a doubt. I guess The grid box has to be formed around the active site residues by changing the x, y and z axis values so that the interaction can be calculated correctly,
@@saikatmandal929 I understood that you don't have to use vina.exe but directly autogrid4 and autodock 4 on autpdock tool. But when I try to put the new parameters the program doesn't run
If I use a receptor that I have already known the binding site with a reference ligand, how can I set the grid box in that binding site only for docking with other molecules?
Sir, I downloaded autodock-vina from the link but after installing the program, it does not have the brown ribbon you used to save the protein and ligand, what should I do?
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?
Thank you so much for your video Dr. Sanket. Firstly I hope you are healthy and safe. I'm trying to perform a molecular docking but I have an error while trying to save the PDBQT file: Unable to assign HAD type to atom Mg Unable to assign valence to atom protein:B: MG2003:MG type = Mg Unable to assign HAD type to atom Mg Unable to assign valence to atom protein:D: MG2003:MG type = Mg By any chance, do you know how to solve it? Thank you so much in advance!
Hi! very helpful video indeed. I have one query which is my SDF file is not getting recognized as a SQLCE database. how do i overcome this error? Kindly help..
Hi! Thank you very much. i learned a lot from your tutorial. May I ask, how can I specify the number of docking runs in Autodock Vina? Is it possible? Coz I am planning to dock at 70 runs.
Hi, I have a issue. I'm not able to get docking results as it show error like, FATAL ERROR: ERROR: 3778 records read in, but only dimensioned for 2048. Change "MAX_RECORDS" in "constants.h". Can u please suggest how to rectify this error ?
Great job dear Prof. highly appreciated. I am quite new to molecular docking and trying to perform docking of activated carbon and a drug using your video as a guide. Will it be possible?
Hello Sir! thank you for your videos,i have a question ,when i drug the pdb files into Autodocktools software,it occurs a error “4mzi.pdb does not exists”,hope you can help me to solve this problem,thank you!
hii.. I need your help. everytime I am trying to save as pdbqt format, my file is being saved as pdf.. could you please tell how to resolve this problem
i use pyrx for docking, and use multiple ligands i download them from zinc database (nubben database for natural compounds), i do minimization and docking but when finish the result are encodede for the compound it just codded the energy , and they are 2332 compound how can i know the compound crosspend to each result???
Sir suupose hum ek research article likh rahe hain , sir kya hum comparison ke liye aesa kar sakte hain kya, jese remdesivir ke liye dimension xyz alag rakh rahe hain isme humne docking autodock vina , command prompt waale step se docking ki , or other multiple ligands ke liye humne autodock vina , command prompt se docking nahi ki more than two ligands hone ke usse , isme humne pyrx virtual screening ka use kiya or dimension xyz bhi different rakhi as compare to remdesivir... To sir kya hum comparison kar sakte hain ab remdesivir or ye multiple ligands kaa.... Yaa hume sabhi ligands ke liye pyrx virtual screening he krni pdegi , agar hum research article m isko publish karana chahte hain to.... Sir koi problem create to nahi hogi dimension different rakhkr comparison kiya karkr
Hello sir, I'm from bioanalytical Sciences ... We had your workshop that I couldn't attend because of personal problems n we have this docking by autodock vina in our practicals n we have our practicals from 8 ... N I'm having some major issues... Whenever I try to download protein it gets downloaded in rasmol raswin than pdb extension .... N ligand in sdf where it supposed to be downloaded in MDL sdf format n because of it I'm not able to proceed ... Can you please suggest me what can be done ?
can anyone please explain my following question? this particular protein "4mzi" in this video has some missing residues in its side chain. so is it possible to do docking without fixing it ? in this mgl tool he didnt fix the missing residue. will that make good docking ?
sir same dimensions rakhne main result alag alag kyu aata hai, jese maine ek ligand ke liye dimension x, y, z 30,40,50 rakhi or binding energy 10 aare h autodock vina se, but jab main yahi dimension rakhta hu same lifand ke liye, par is time main pyrx virtual screening tool se karta hu to result 9 binding energy kyu aata hai
Sir few docking files in the folder remain hidden and no matter what I do, I'm not able to view them in the Docking folder. It's visible in AutoDock when I select Read Molecule but not in the folder. How do I resolve this sir?
Hey very nice and clear presentation. Wanted to ask one question so the final poses that you visualise in pymol and if we suppose find the first pose as the best docking pose how do we save it and use for showing it in power point?
Respected sir need help The command shows the program is not recognized as an internal or external command operable program or batch file what is the solution for this problem
my protein doesnot contain cl atom which is there in the ligand and maps are generated for all atoms in the protein. while autodocking its showing the error: I'm sorry; I can't find or open "5nm2.Cl.map" the atoms in protein are : A C H HD N OA SA and atoms in ligand are:A Cl OA N pls tell how remove the error
Hi Sanket in Ur video you have not mentioned the path of folders where we must keep the files to run autodock, when I am running auto dock it showing error
Sir.. Everything is useful in this video. But am unable to download PyMOL. My system can't allow that to instal. So, kindly send the ligand format file, sir.
Thanks for such a nicely presented video, especially for beginners. However, during the protein and ligand preparations, i am unable to save file in pdbqt format. kindly guide through some tips, which could work for me
why you have not deleted zinc metal in the protein during protein preparation,any reason behind this??? If i delete any problem ? can you explain? I shall be thankful to you
thank u Sanket B.. excellent and more useful both of docking videos
Thank you very much!
I think I'll put your name in acknowledgment, you are the only one who helped me in learning which I was roaming around behind everyone... Thanks
I never thought i'll enjoy learning simulations so much. Thank you for making it so simple and easy. :)
These two videos have been really helpful for my work. Thank you so much.
This has been highly informative so far, thanks for the refresher!
hello, i find molecular dynamics hard to learn as i had no prior experience with coding and linux (what my teacher recommended me to use), videos like this makes it very easy for me to understand the concept and how to do it. THANK YOU FOR THE VIDEO!
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Sir, at 9:25 you add Kollman charges to the protein. However, at 15:23, when you load the protein macromolecule, you click on 'no' for preserving Kollman charges. The next popup box states that Gasteiger charges were added. So, should we add Gasteiger charges for the protein?
At 17:55, Spacing parameter is set 0.375 A, but this is not used by AutoDock VINA. Changing this parameter affects the grid box size. So even you attempt to perform site specific docking, the docking is going to be blind docking due to this parameter. I am not able to get the clarification about this parameter while docking except VINA official tutorial has this option set as 1.
i want to give you the credit if I got a paper published like literally ...Extremely helpful
the best video i have ever watched so far
thanks a lot for your kind efforts
Very useful both parts for autodock vina learning
Hello Sir! How to prepare script for multiple ligand docking?
Yes please!
superb video..your way of explaination is so clear
Can anyone help me out with the installation , I seem to have problem with finding the vina folder in the path hence not able to attempt docking
you are doing grat job. Could you prepare a molecular docking video for ligand-based drug design.
I love this. It is so helpful and explanatory.
It says could not open "config.txt" for reading while clicking enter from (8:35). Please help
thank you sir , you explained each and every step very clear .
You are doing a very good job. Keep it up Dr.
This video series help me a lot
Great tutirial and very informative one. Kindly if possible add ligand and DNA docking tutotrial. Sir it would be great job on your part. Thanks regards
Thank you Sanket Bapat. Both the videos are very neatly and clearly presented. Highly informative. But once after docking how are we to interpret it in the paper. Any suggestions or advice regarding the same.
this video is a life saver thank you so much !!!
Very nice video sir.... Ur explanation was very clear ... Thanks a lot sir
like your tutorial video sir, very helpful.
Thank you so much 😇🙏
Hi thanks for this, came at the right time! When adding the grid box, is it generated automatically at the binding pocket or will have to adjust it? if so, how do i ensure its the 'correct' coordinates?
from literature you have to search
What about chimera or autodock and pymol is more effective...thank so much Dr.sankat🎉🎉😊
Thank you sir for such a nice video. One question- if we don't know the active site, why we are not enclosing the whole protein inside the grid by changing dimensions.?
Good question, yes we can encompass the whole protein.
Thanks for great tutorails! Small question - why do not you add all hydrogens but only polar ones?
Very well explained .. sir thankyou so much for ur efforts..
Thank you very much!
It's very helpful can make a tutorial or multiple ligand docking and results interpretation on auto dock instead of pymol
Could you make a video showing how to dock in Vina Auto-docking using some flexible active site waste? I need my molecule to interact with specific residues and I don't know how to do it. Please.
Hi joyce I think you cover all the protein by doin grid box so it will be flexible as you took all protein whereever will get less energy it will enter
As we all know that docking simply interaction between receptor and ligand molecule, before docking we do remove the water molecule and some other additional ligands molecule , and add polar hydrogen bond also, Afer that we dock between receptor and ligand molecules, and more negative sign give the good stability.....but sir my question is that in natural condition how water and additional ligands remove from receptor molecules and how will i add polar hydrogen also?
Good day to you sir. Thank you for this excellent interactive session. I have a query, What is to be done if ligand profiles are not seen in the downloaded material from PDB.
It´s so nice your video, Sr! Thank you
Thanks for the amazing explanation
Thank you for your helpful videos Dr. Sanket. I have a question. Is Autodock vina flexible or rigid docking?
Hi very informative tutorial on AutoDock Vina but I have a question which is that what about if we don't know about the ligand binding site of our protein so how can we set the grid?
Should we follow the default grid box dimensions mentioned in the autodock vina ? Wouldn't it be correct if we first checked literature for the docking site and then changed the dimensions of the grid box? Dr. Sanket , could you clarify this ?
Hi Dr. Sanket. I am an IBDP 2 student. For my school project I need to conduct multiple ligand simultaneous docking. I was able to conduct single ligand docking but am unable to understand how to do MLSD. Can you please help with instructions on how to do this. Thank you
Sir, can we used ligand file prepared in autodock tool in Vina and what about energy minimization step?
I have a doubt. I guess The grid box has to be formed around the active site residues by changing the x, y and z axis values so that the interaction can be calculated correctly,
Why do you skip some steps like energy minimization of ligand and protein and charges added to ligand
Hi! Tab with Ligand icon not available to do ligand preperation in MGL tool. Appreciate your help regarding this how to go about
if I follow the step by step of your docking lecture, then can i make the HLA/HLA-DBR and epitope docking properly for vaccine design??
Honestly I appreciate so much your video thank you
Can DNA-Protein docking be performed in Autodock? Please suggest a suitable tool for building DNA 3D structure
Sir, very nice video
Can you please make a video in which you explain how adding a metal ion ( in my case is tin)
I am facing problem for adding pt metal.
@@saikatmandal929 I understood that you don't have to use vina.exe but directly autogrid4 and autodock 4 on autpdock tool. But when I try to put the new parameters the program doesn't run
Devudu swami nuvvu.. 🙏❤
great video content about docking
If I use a receptor that I have already known the binding site with a reference ligand, how can I set the grid box in that binding site only for docking with other molecules?
Is there any rule regarding which chain should be kept and which one should be deleted ?
Sir, I downloaded autodock-vina from the link but after installing the program, it does not have the brown ribbon you used to save the protein and ligand, what should I do?
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?
It is necessary in autodock to kept the torsion agnles of ligand less than 6?
Very informative Sanket B.
Thank you so much for your video Dr. Sanket. Firstly I hope you are healthy and safe. I'm trying to perform a molecular docking but I have an error while trying to save the PDBQT file:
Unable to assign HAD type to atom Mg
Unable to assign valence to atom protein:B: MG2003:MG type = Mg
Unable to assign HAD type to atom Mg
Unable to assign valence to atom protein:D: MG2003:MG type = Mg
By any chance, do you know how to solve it?
Thank you so much in advance!
Cyp 17 ko pyrx virtual screen tool main upload karne se alternate conformation bata raha hai, or pdbqt file main convert nahi ho raha hai....
Hi! very helpful video indeed. I have one query which is my SDF file is not getting recognized as a SQLCE database. how do i overcome this error? Kindly help..
Hi! Thank you very much. i learned a lot from your tutorial. May I ask, how can I specify the number of docking runs in Autodock Vina? Is it possible? Coz I am planning to dock at 70 runs.
Hi, I have a issue. I'm not able to get docking results as it show error like, FATAL ERROR: ERROR: 3778 records read in, but only dimensioned for 2048.
Change "MAX_RECORDS" in "constants.h".
Can u please suggest how to rectify this error ?
Great job dear Prof. highly appreciated. I am quite new to molecular docking and trying to perform docking of activated carbon and a drug using your video as a guide. Will it be possible?
Hello Sir! thank you for your videos,i have a question ,when i drug the pdb files into Autodocktools software,it occurs a error “4mzi.pdb does not exists”,hope you can help me to solve this problem,thank you!
I have installed autodock vina, but it is not working. would you please share the alternate link?
Amazing it's educating thanks
sir can you please tell me how to determine mutation rate of covid19 using bioinformatics tool? and which tool can be used?
hii.. I need your help. everytime I am trying to save as pdbqt format, my file is being saved as pdf.. could you please tell how to resolve this
problem
i use pyrx for docking, and use multiple ligands i download them from zinc database (nubben database for natural compounds), i do minimization and docking but when finish the result are encodede for the compound it just codded the energy , and they are 2332 compound how can i know the compound crosspend to each result???
you are just pathfinder for bioinformatics learner.
Thank you very much, well explained. Is the Auto dock vina App free?
Sir suupose hum ek research article likh rahe hain , sir kya hum comparison ke liye aesa kar sakte hain kya, jese remdesivir ke liye dimension xyz alag rakh rahe hain isme humne docking autodock vina , command prompt waale step se docking ki , or other multiple ligands ke liye humne autodock vina , command prompt se docking nahi ki more than two ligands hone ke usse , isme humne pyrx virtual screening ka use kiya or dimension xyz bhi different rakhi as compare to remdesivir...
To sir kya hum comparison kar sakte hain ab remdesivir or ye multiple ligands kaa.... Yaa hume sabhi ligands ke liye pyrx virtual screening he krni pdegi , agar hum research article m isko publish karana chahte hain to.... Sir koi problem create to nahi hogi dimension different rakhkr comparison kiya karkr
Hello sir, I'm from bioanalytical Sciences ... We had your workshop that I couldn't attend because of personal problems n we have this docking by autodock vina in our practicals n we have our practicals from 8 ... N I'm having some major issues... Whenever I try to download protein it gets downloaded in rasmol raswin than pdb extension .... N ligand in sdf where it supposed to be downloaded in MDL sdf format n because of it I'm not able to proceed ... Can you please suggest me what can be done ?
can anyone please explain my following question? this particular protein "4mzi" in this video has some missing residues in its side chain. so is it possible to do docking without fixing it ? in this mgl tool he didnt fix the missing residue. will that make good docking ?
sir same dimensions rakhne main result alag alag kyu aata hai, jese maine ek ligand ke liye dimension x, y, z 30,40,50 rakhi or binding energy 10 aare h autodock vina se, but jab main yahi dimension rakhta hu same lifand ke liye, par is time main pyrx virtual screening tool se karta hu to result 9 binding energy kyu aata hai
Can we perform docking with metal complexes ( Pt complex)?
sir I wanted to know..if the same thing can be executed in ubuntu system
Sir few docking files in the folder remain hidden and no matter what I do, I'm not able to view them in the Docking folder. It's visible in AutoDock when I select Read Molecule but not in the folder. How do I resolve this sir?
Hi Sanket, do you know how to calculate the binding constant or inhibition constant?
Can you please let me know why do we add polar hydrogens and kollman charges?
Cant I do docking in the autodock tool instead of prompt command?
Hey very nice and clear presentation. Wanted to ask one question so the final poses that you visualise in pymol and if we suppose find the first pose as the best docking pose how do we save it and use for showing it in power point?
You can download the pdb file of the first pose, and then take an image of it.
Very well explained sir
Respected sir need help
The command shows the program is not recognized as an internal or external command operable program or batch file
what is the solution for this problem
my protein doesnot contain cl atom which is there in the ligand and maps are generated for all atoms in the protein. while autodocking its showing the error: I'm sorry; I can't find or open "5nm2.Cl.map"
the atoms in protein are : A C H HD N OA SA and atoms in ligand are:A Cl OA N
pls tell how remove the error
Hi Sanket in Ur video you have not mentioned the path of folders where we must keep the files to run autodock, when I am running auto dock it showing error
If you see the video I had created the folder on Desktop, you can create your destination folder anywhere you want.
I have done docking in vina by coding only..autodock is GUI, isn't Vina acessesd by coding only?
In docking...grid macromolecule protein are choose..then show error....so, what do i do now....
Plss..help me..
Sir, Amber 18 pe kaise simulation hota hai....iska video banaiye kabhi 🙏
Very nice information Dr. Gajanan Dongare Akola Maharashtra
my protein file is not saveing as the pdbqt so what should i do
Sir.. Everything is useful in this video. But am unable to download PyMOL. My system can't allow that to instal. So, kindly send the ligand format file, sir.
Thanks for such a nicely presented video, especially for beginners.
However, during the protein and ligand preparations, i am unable to save file in pdbqt format.
kindly guide through some tips, which could work for me
Same with me sir, please guide us.
I was done project work the same topic Sir.
My pdb file is getting downloaded in the form to words how can I get in form of image
why you have not deleted zinc metal in the protein during protein preparation,any reason behind this??? If i delete any problem ? can you explain? I shall be thankful to you
Sometimes metal ions can play significant role in docking, so when you consider a protein for docking know whether ions are important or no
Sir plz make a video of docking by arguslab ...i really need it now
Sir,can you tell how to determine ki for inhibitors using autodock
Thanks for this video!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! I love you
Thank you doctor🎉
Can u please recommend which server is best for blind docking.....
Try easydockingvina it's a software