Molecular Dynamic Simulation Online (Part 1)|Ligand-target interaction|iMODS tutorial

Online molecular dynamic simulation (MD simulations) by using iMODS online web server. Preparing files in PDB format in discovery studio visualizer after docking studies for ligand-target interaction, DNA-protein interaction and computer-aided drug design ‪@MajidAli2020‬

[@rimshakhushal174]

Informative👍

[@learnwithtricksandfun4876]

Phenomenal 👍👍

[@rashamoustafa427]

This is magnificent 👏 👌 🙌 gurgas fantastic 👏 lecture Doctor blesses by Allaha and may all your days be great 👍

[@MKSILVA8405]

Are you able to access iMODS?

[@NessaibiaHanen]

Please give me the correct link of iMods. I couldn't get into it

[@NessaibiaHanen]

Please give me the correct link of iMods. I couldn't get into it

[@ouidedbenslama783]

مشاء الله ربي يزيدك علما و يجعلها في ميزان حسناتك

[@eshajadoon8492]

👏👏

[@ProfAhmedALi]

Very clear

[@ayeshaabrar7523]

👍👍

[@ارشدشعیب]

MashaAllah 💞

[@MajidAli2020]

Thanks

[@ارشدشعیب]

@@MajidAli2020 welcome sir 💞💞

[@-SaeedKhan]

👌

[@imranchemist7342]

MashAllah very Informative video..
How to obtain those graphs in which nanonscanes are mentioned.?

[@-Saadff]

👍

[@sriknathpenumala5258]

Sir but in complex ligand is not visible in imod web server

[@bemotivate4938]

How to make √3 × √3 surface model of any matel

[@jeevakanthv]

I didn't get proper link. Put how to download video pls

[@biomedicalscientistmuhammad]

but dear dr why the ligand do not appear !!

[@MajidAli2020]

It appears look in part 2

[@biomedicalscientistmuhammad]

Can i plot rmsd using the data i get ?

[@biomedicalscientistmuhammad]

and how can i get a vedio for my simulation

[@adeelakram3811]

i perform all steps but iMODS show error no job done

[@jaweriabatool4318]

Lkn server download Kahan se krna???

[@MajidAli2020]

Use it online

[@mdhasanali3158]

how can i open iMODS server?

[@NessaibiaHanen]

Please give me the correct link of iModS. I couldn't get into it

[@MajidAli2020]

Search in google u will get it

[@NessaibiaHanen]

I didn't find it

[@samsoonmaharifa6687]

Sir I am not able to save the ligand protein complex as pdb file in DSV
Can you help to trouble shoot it?
Thank you

[@MajidAli2020]

Sure

[@adeelakram3811]

have same problem, it only consider protein

[@MajidAli2020]

Look at my second video of MD simulation it will clear ur concepts more

[@samsoonmaharifa6687]

Thank you

[@anila5561]

If we made a structure in MS then how it is export and save a high quality image through DSV

[@MajidAli2020]

First open it in DSV and then save image

[@anila5561]

@@MajidAli2020 i have opened the image in DSV but the save option and visualization options are inactive

[@MajidAli2020]

You have to open file in pdb, mol2 or dsv in DSV then save as image file

[@anila5561]

Sir I have done MD simulation but after 2500 fs the energy is changed , lower than straight line. How can we justify this or check the bond length changes with time

[@MajidAli2020]

Where did u perform and which software u used

[@anila5561]

@@MajidAli2020 Im using vasp to perform MD simulations

[@BabyDoll-rp4jr]

Sir, iMODS mn prepared protein open karn ya PDB format mn downloaded protein qk Meri protein mn missing residue bi boht thy mn ny modified ke or phr protein prepared ke..
Kindly assist me out there; Thanks

[@MajidAli2020]

Missing residues will remain as such either u open in PDB or not

[@guglielmopaganetto]

I perform all steps of Part 1 but this error appears: Error /var/www/imod/Results/job0306112031129 Can NOT been created!
Thank you

[@hafsaishfaq4574]

👍👍

[@-LaibaPrincess]

👍

[@-AimenWajid]

👍👍