Thank you so much sir, I'm really introvert this is the first time in my life that I'm commenting on any video. But, really wanna thank you. All of your videos made my project so easy that I got full marks and all worked so well. I performed complete CADD just through your videos. Really appreciate your great work 😊
Sir thanks for sharing knowledge..Sir kindly make videos on md simulation through Gromacs, Amber or NAMD..Although there are lots of videos on RUclips..but your teaching method is too good..So, it's my humble request Sir plz
I perfpermed this molecular dynamics simulations and I used my complex, but not that the way you performed in Chimera sir, I perfoermd in pyrx and discovery studio, from.there I got my ligand-protein complex file. And I uploaded here. I got the same results in iMODS, but sir after this how to check the tgz file, and this is all about molecular dynamics simulations or any further step is there in this? Please guide me sir.
Sir, I have uploaded my pdb file of the receptor-vaccine docked complex on imod and got my result in one day. However, after one day the link of the result is showing site cannot be reached. I had to upload the pdb file again.The result is not coming yet since three days. The Imod job id is still running. What should I do? How much more time will it take for the results to come? also why is it taking more days now to give the result???
Sir could you please name some simulation tools which I can use in publications (with acceptable certainties) other than GROMAC (because I don’t know how to use Unix OS)?
Sir jese hum docking karte time receptor protein kaa interaction karte hain , us time receptor protein kaa water remove karte hain, or ligand kaa interaction karte hain, but natural condition main recepror protein main water rahega, phir interaction kese hoga..... Sir plz doubt clear kar dijiye .... Usually water active site ko distort krta h interaction ke time, tbhi hum water molecules ko remove karte hain , but jab hum koi medicine/ligand create kar lenge to wo to phir body ke inside receptor protein main water hone se interaction hi nahi hone dega natural condition main..... Plz clear the doubt of my question sir .....
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?
@@Prof.Dr.MuhammadNaveed Hello Sir, This is nice presentation. I am facing problem in opening seed1.crd file in chimera. If this is PC error, how to remove this, sir?
thanks for sharing such quick method for beginners , Sir in case if we are doing docking via MOE , then how can we upload the complex file on iMODS. Kindly guide in that perspective
Sir docking MOE pe best nahe hai kia? Manual process hai wo zaida acceptable hoga thesis me?? MOE pe docking karai please, and gromacs pe m.d simulations
sir swissdock shows that i have a protein of more than 15000 atoms so i should truncate my protein although there is no water molecule and extra ligands . what does it mean and what should i do?
Sir, whenever uploaded PDB file in iMOD server, everytime shows not valid pdb file, but the pdb file is ok. Would you please help me on it and is there any issue on the server, because such type of pdb file is shown the result earlier in the iMOD server.
Sir mene simulation ki hy. But graph me pdb ki black line show ni hoti meri ksi b simulation me. Just red lines show ho rae hain... Kindly guide me k wo show kyu ni ho rae?
Hello sir, the presentation is really good. I have one query. I performed the same protocol that you shared here for IMOD. but somehow, I failed somewhere, I couldn't see the two peaks in the distance profile and B-factor. It would be so great if you could help me with this.
Sir predicted file direct chimera pr open ni ho ri... Seed1 download kr k jab file chimera pr open ki jati hy to file type select krny ka option ata hy.. Vahan sy crd file jo k seed 1 ki hy ..is k liy konc file type select ki jy?
Thank you so much sir, I'm really introvert this is the first time in my life that I'm commenting on any video. But, really wanna thank you. All of your videos made my project so easy that I got full marks and all worked so well. I performed complete CADD just through your videos.
Really appreciate your great work 😊
Sir thanks for sharing knowledge..Sir kindly make videos on md simulation through Gromacs, Amber or NAMD..Although there are lots of videos on RUclips..but your teaching method is too good..So, it's my humble request Sir plz
Please tell how to open Swiss dock file in UCFF chimera?
I perfpermed this molecular dynamics simulations and I used my complex, but not that the way you performed in Chimera sir, I perfoermd in pyrx and discovery studio, from.there I got my ligand-protein complex file. And I uploaded here. I got the same results in iMODS, but sir after this how to check the tgz file, and this is all about molecular dynamics simulations or any further step is there in this? Please guide me sir.
for basic this is all but for more improvement need GROMACS
Sir I upload docked complex of my protein model..In B factor pdb graph is not showing , only NMA graph is there
Run again
Sir!How to open prediction file into UCSF chimera ?I have downloaded r install chimera but unable to open this prediction file
follow as i did
Sir pls help me ……my cluster file is not opening by chimera pls help me sir how to open this
Sir, I have uploaded my pdb file of the receptor-vaccine docked complex on imod and got my result in one day. However, after one day the link of the result is showing site cannot be reached. I had to upload the pdb file again.The result is not coming yet since three days. The Imod job id is still running. What should I do? How much more time will it take for the results to come? also why is it taking more days now to give the result???
I think due to overload so need to do again after some days
@@Prof.Dr.MuhammadNaveed Thank you Sir for your reply.
Excellent..
Glad it was helpful!
Aoa Sir I have done simulation with same protein but different ligands but problem is that results are same for all Ligands why??
Sir could you please name some simulation tools which I can use in publications (with acceptable certainties) other than GROMAC (because I don’t know how to use Unix OS)?
simlab
Sir jese hum docking karte time receptor protein kaa interaction karte hain , us time receptor protein kaa water remove karte hain, or ligand kaa interaction karte hain, but natural condition main recepror protein main water rahega, phir interaction kese hoga..... Sir plz doubt clear kar dijiye .... Usually water active site ko distort krta h interaction ke time, tbhi hum water molecules ko remove karte hain , but jab hum koi medicine/ligand create kar lenge to wo to phir body ke inside receptor protein main water hone se interaction hi nahi hone dega natural condition main..... Plz clear the doubt of my question sir .....
they cope with many other interaction in body
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?
docking not possible in natural by you as this happened by nature but we opt all condition in dry lab to get natural results
Thank you sir
you r the best
pleasures
Sir! If the result of Pbd and NMD is not similar.all other result are good
Then what I need to do?
then you go ahead
sir how did you open the the seed1.crd file in chimera. I am not able to open it .It is showing to choose file type
then your PC error
@@Prof.Dr.MuhammadNaveed Hello Sir, This is nice presentation. I am facing problem in opening seed1.crd file in chimera. If this is PC error, how to remove this, sir?
Does Gromac and AMBER give better MD simulation result compared to Imod?
yes definitely but here used online tool for beginners
Dear sir, when we upload the protein ligand complex, in results it doesn't show separate markers.?
do check complex first then upload
thanks for sharing such quick method for beginners , Sir in case if we are doing docking via MOE , then how can we upload the complex file on iMODS. Kindly guide in that perspective
do as did for vina
How You open the Seed.1.crd in Chimera??? Kindly tell me, please..
follow lecture
Why IMODS server is not opening anymore? Can anyone suggest a better option?
Aslam o Alikum, Sir MA iMode ko stimulation analysis KY lye try kr rhi lakn nah chal rha kya kro. Please reply me.
Sir docking MOE pe best nahe hai kia? Manual process hai wo zaida acceptable hoga thesis me?? MOE pe docking karai please, and gromacs pe m.d simulations
yes noted but here use online tools which are well cited
@@Prof.Dr.MuhammadNaveed sir auto dock vina ka koi easy way nahe hai? Agr hai tu please os pe ek lecturer krwai....
Sir, For Antibody Engineering please give lecture on this and online tools to perform antibody engineering.
noted
@@Prof.Dr.MuhammadNaveed Thank you so much sir for your reply.
Sir which one is best for molecular docking autodock or swissdocking?
sir swissdock shows that i have a protein of more than 15000 atoms so i should truncate my protein although there is no water molecule and extra ligands . what does it mean and what should i do?
remove the unnecessary chains from protein.
Sir iMOD surver show error massage when I uploaded protein ligand complex downloaded from SWISS DOCK.
How to solve this problem
Plz replies
link down and wait to be active
Sir, whenever uploaded PDB file in iMOD server, everytime shows not valid pdb file, but the pdb file is ok. Would you please help me on it and is there any issue on the server, because such type of pdb file is shown the result earlier in the iMOD server.
link down
@@Prof.Dr.MuhammadNaveed sir, please make a video on MD simulation (web server based like simlab). Thanks
Sir.. why imods is not working these days..
Sir,I have completed docking using Patch dock but imods showing error.What should I do?
do with autodock then imods
Sir any bioinformatics tool specific for promoter analysis of fungus
many but you may follow this
ruclips.net/video/LC__PSVsjxw/видео.html
A.o.a sir g ham na docking pyrx k through ki hy us men docked complex kasa save how gay
Tq sir
Sir mene simulation ki hy. But graph me pdb ki black line show ni hoti meri ksi b simulation me. Just red lines show ho rae hain... Kindly guide me k wo show kyu ni ho rae?
use screenshot of original
sir yeh simulation protein-protein k liye bhe use ki ja skti?
thanks you very much sir
All the best
In other MD simulations, they performed on ns , simulation time. What about imod?
algorithm design on standard ns
@@Prof.Dr.MuhammadNaveed
Approximately how many ns?
Sir kindly tell any substitute tool for imod?
Hello sir, the presentation is really good. I have one query. I performed the same protocol that you shared here for IMOD. but somehow, I failed somewhere, I couldn't see the two peaks in the distance profile and B-factor. It would be so great if you could help me with this.
then first check you docked complex interactions
@@Prof.Dr.MuhammadNaveed i have checked.. but still it's not working
very helpful
Glad to hear that
Which one is better for md simulation vmd/NAMD or Gromac or online server ( Imod)
GROMACS
Whatever result we r getting from IMODS can we publish in research paper
sure
Sir predicted file direct chimera pr open ni ho ri...
Seed1 download kr k jab file chimera pr open ki jati hy to file type select krny ka option ata hy.. Vahan sy crd file jo k seed 1 ki hy ..is k liy konc file type select ki jy?
pdb or follow as i did
The link is down, is there another link ?
no dear
sir ap ny Jo Jo step btya unko fellow kia imod k result aa raha graph but Jo first page pa protein k structure hai vo ni aa raha ...plzz guid kar dy
run again
Sir, How you predicted that seed 1 has the lowest energy. Waiting for your reply Sir
based on results of complex
Sir. Can we perform MD Simulation when inhibitor is non-competitive in nature ?
And kindly elaborate on the discussion about the results of MD simulation (this video).
yes and sure will do in coming lectures
sir from where did you inference target ?? from step 2
on the basis of ligand
oky sir thankuh, sir please guide how to open seed crd file using chimera
Sir could you please provide literature of yours where you had shown md simulations ?
literature ?
@@Prof.Dr.MuhammadNaveed yes sir
Can i use this in thesis ?
And how we find residuals interaction of imod simulation.
by graphs can analyze
Sir can we put imod simulation in our manuscript if yes please share manuscript.
yes you can and literature available on iMOD homepage
Sir what is the best docking software ?
autodock vina
Thank you sir
is simulation required super Computer?
not all
Sir kindly share any paper from which i can see how to properly interpret it...
Sars cov2 vaccine design by Muhammad Naveed search from google
Rmsd value sir
IMods Is not working sir and not giving results
server down
Sir how to find traget
on the basis of ligand
I used imode and it show that there is no b factors in my molecule
run again to confirm
Unable to open seed file ,please help sir
do try again
👍
that dont work
Can you please do this in eglish or add English subtitles 🙏
sure, will add subtitles
Great but talking english clear in not quick 😊🎉🎉🎉🎉
Chimera is unable to open the seed crd file , what should I have to do??
server down