thanks a lot for the wonderfull explaination.Can you please guide how we can visualize the hydrogen and hydrophobic interections using Mypresto portal.How to use find pocket if the receptor protein lacks ligand
Thank you very much! I am glad that you liked it. You can find the answer to all your questions in this manual: www.moldesk.com/wp-content/uploads/2022/05/MolDesk_Basic_ver.1.1_Manual_en.pdf Please feel free to contact me in the future! All the best!
To run longer trajectory, you have to increase the MD (steps). Let's say i want to run for 200ns. Then what should be the number of steps? Moreover, how many hours will it take on a regular computer?
It will take a lot of time on a regular computer. My recommendation would be to use the free CLI version myPresto software (www.mypresto5.jp/en/) on a supercomputer or workstation to run the simulation. Please feel free to contact me in the future! All the best!
Thank you so much for introducing us with such a wonderful software. Ma'am, would you make a video on how to analysis the MD stimulation data of Mypresto portal in VMD software and also a video on how to get a paid version of Mypresto portal software.
Thank you very much! I am glad that you liked it. You can find the answer to all your questions in this manual: www.moldesk.com/wp-content/uploads/2022/05/MolDesk_Basic_ver.1.1_Manual_en.pdf You can purchase the paid GUI version Moldesk (www.moldesk.com/). Please feel free to contact me in the future! All the best!
Thank you very much Madam.... Well explained..... Have one query mam! If we want to load protein and ligand molecules separately, how to do it? Protein import is happening but facing problem in import of ligand into tutorial .. Thank you Mam
Thank you! After importing protein, go to "Design" tab in "Command View", then ligand can be imported in two ways: 1) Click "Add Remote Compound", and enter PubChem ID or KEGG DRUG ID or LigandBox ID of ligand. [Be sure to choose 3D (or else you will import 2D ligand and it will cause error)]. 2) If you already have 3D structure of ligand in format supported by myPresto portal (.pdb, .mol2 or other format), then you can import it by clicking on "Insert from file". I hope this will help you import the ligand. If you have further queries, please feel free to ask.
@@MysteryMohini7 Many thanks Madam. I got it. Now I can able to run the files and got output file also. But have one more query! How to fix grid box size if we know the X, Y, Z axis instead of using make pocket through other ligand co-ordinates? Thank you Madam...
@@ashvinkumarkatral1978 1)Go to "Dock" tab in "Command View". 2) Select your protein and click on "Make Pocket" and then you can add X, Y, Z coordinates and select the radius of the pocket. I hope this will help you make the pocket. If you have further queries, please feel free to ask. Thank you!
@Mohini Mam.... What should be the minimum fsec in time step? Is 1 fsec= 1 nano second? or how to increase the exposure time till 50 or 100 nano seconds? Thank you Madam
@@ashvinkumarkatral1978 fsec is femtosecond. 1 nanosecond (ns) = 1000000 femtosecond (fs) 2 fsec is a good time step. To run longer trajectory, you have to increase the MD(steps). But it will take a very long time to run till 50 or 100 ns on a normal computer. If you have further queries, please feel free to ask. Thank you!
Thank you very much, but I have a question... this is a good software and it is easy to work with... but what is the problem that it is not used in the articles and I have not seen its name in any article yet🤔🤔🤔
Thank you!!! Yes, you can extract the trajectory by selecting both the protein and ligand and then going to "File" and clicking on "Export Trajectory" or "Export PDB". Then, you can visualize that trajectory in another softwares like VMD.
Thank you so much for this brilliant tutorial. Though I'm facing a problem while exporting the trajectory and uploading it in VMD. the VMD software is not accepting the file while loading. I found out that the trajectory file output is in PRESTO format, but there in nothing like this option in VMD while loading. So, can you help me with the conversion needed between these two steps?
Thank you!!! In myPresto Portal, after selecting your protein or ligand or both, go to "File" and select "Export PDB". This will export trajectory in PDB format and then you can open it in VMD.
Ma'am, I have a question. Can we use this portal for MD simulation of Protein-protein docked structure? I have the pdb file of the docked molecule and want to do the simulation part only. Is that possible?
If the ligand weight is more than 400, you can't perform the docking or simulation on myPresto portal. You have to either purchase the paid version GUI Moldesk (www.moldesk.com/) or use free CLI myPresto software (www.mypresto5.jp/en/). Please feel free to contact me in the future! All the best!
If the number of atoms is more than 25000, you can't perform the docking or simulation on myPresto portal. You have to either purchase the paid version GUI Moldesk (www.moldesk.com/) or use free CLI myPresto software (www.mypresto5.jp/en/). Please feel free to contact me in the future! All the best!
Thank you!!! In myPresto Portal, after selecting your protein or ligand or both, go to "File" and select "Export PDB". This will export trajectory in PDB format and then you can open it in VMD. After opening PDB file in VMD, go to "Extensions", go to "Analysis", then select "RMSD Calculator", "RMSD Trajectory Tool", or "RMSD Visualizer Tool" to check RMSD.
Ma'am please share your email or mobile no I want to ask related to docking and MD simulation
Please feel free to contact me on LinkedIn (www.linkedin.com/in/mohini-yadav-engd-31305383/ ) or by email (ymohini.yadav@gmail.com).
Thank you!
This is the best tutorial ever; thank you, Miss Yadav.
Thank you very much. The tutorial is really appreciated. Best regards from Yemen.
Thank you 💜
Thanks a lot Mohini for this fruitful and wonderful tutorial which solv many questions and problems I had faced
Thank you very much! I am glad that you like it.
Please feel free to contact me in the future!
All the best!
thanks a lot for the wonderfull explaination.Can you please guide how we can visualize the hydrogen and hydrophobic interections using Mypresto portal.How to use find pocket if the receptor protein lacks ligand
Thank you very much! I am glad that you liked it.
You can find the answer to all your questions in this manual: www.moldesk.com/wp-content/uploads/2022/05/MolDesk_Basic_ver.1.1_Manual_en.pdf
Please feel free to contact me in the future!
All the best!
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
To run longer trajectory, you have to increase the MD (steps). Let's say i want to run for 200ns. Then what should be the number of steps? Moreover, how many hours will it take on a regular computer?
It will take a lot of time on a regular computer. My recommendation would be to use the free CLI version myPresto software (www.mypresto5.jp/en/) on a supercomputer or workstation to run the simulation.
Please feel free to contact me in the future!
All the best!
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Thank you so much for introducing us with such a wonderful software. Ma'am, would you make a video on how to analysis the MD stimulation data of Mypresto portal in VMD software and also a video on how to get a paid version of Mypresto portal software.
Thank you very much! I am glad that you liked it.
You can find the answer to all your questions in this manual: www.moldesk.com/wp-content/uploads/2022/05/MolDesk_Basic_ver.1.1_Manual_en.pdf
You can purchase the paid GUI version Moldesk (www.moldesk.com/).
Please feel free to contact me in the future!
All the best!
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Thank you Mohini for wonderful information it's really helpful for me
Thank you very much! I am glad that you like it.
Please feel free to contact me in the future!
All the best!
Thank you very much Madam.... Well explained.....
Have one query mam!
If we want to load protein and ligand molecules separately, how to do it? Protein import is happening but facing problem in import of ligand into tutorial .. Thank you Mam
Thank you!
After importing protein, go to "Design" tab in "Command View", then ligand can be imported in two ways:
1) Click "Add Remote Compound", and enter PubChem ID or KEGG DRUG ID or LigandBox ID of ligand. [Be sure to choose 3D (or else you will import 2D ligand and it will cause error)].
2) If you already have 3D structure of ligand in format supported by myPresto portal (.pdb, .mol2 or other format), then you can import it by clicking on "Insert from file".
I hope this will help you import the ligand. If you have further queries, please feel free to ask.
@@MysteryMohini7 Many thanks Madam. I got it. Now I can able to run the files and got output file also.
But have one more query! How to fix grid box size if we know the X, Y, Z axis instead of using make pocket through other ligand co-ordinates? Thank you Madam...
@@ashvinkumarkatral1978
1)Go to "Dock" tab in "Command View".
2) Select your protein and click on "Make Pocket" and then you can add X, Y, Z coordinates and select the radius of the pocket.
I hope this will help you make the pocket. If you have further queries, please feel free to ask.
Thank you!
@Mohini Mam.... What should be the minimum fsec in time step? Is 1 fsec= 1 nano second? or how to increase the exposure time till 50 or 100 nano seconds? Thank you Madam
@@ashvinkumarkatral1978
fsec is femtosecond.
1 nanosecond (ns) = 1000000 femtosecond (fs)
2 fsec is a good time step.
To run longer trajectory, you have to increase the MD(steps). But it will take a very long time to run till 50 or 100 ns on a normal computer.
If you have further queries, please feel free to ask. Thank you!
Thank you very much, but I have a question... this is a good software and it is easy to work with... but what is the problem that it is not used in the articles and I have not seen its name in any article yet🤔🤔🤔
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Ma'am can you please tell me how I can shorten my protein using MD simulation and then how I can improve its stability and activity?
Please email me (ymohini.yadav@gmail.com) your query! I will reply to you ASAP! Thank You! ☺
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
ma'am, thank you so much for sharing.
Thank you very much! I am glad that you like it.
Please feel free to contact me in the future!
All the best!
Maam, i am not getting any result after docking.
Very Nice tutorial Mohini...I have a question, can we extract the trajectory from this free software for the analysis in VMD?
Thank you!!!
Yes, you can extract the trajectory by selecting both the protein and ligand and then going to "File" and clicking on "Export Trajectory" or "Export PDB". Then, you can visualize that trajectory in another softwares like VMD.
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Thank you so much for this brilliant tutorial. Though I'm facing a problem while exporting the trajectory and uploading it in VMD. the VMD software is not accepting the file while loading. I found out that the trajectory file output is in PRESTO format, but there in nothing like this option in VMD while loading. So, can you help me with the conversion needed between these two steps?
Thank you!!!
In myPresto Portal, after selecting your protein or ligand or both, go to "File" and select "Export PDB". This will export trajectory in PDB format and then you can open it in VMD.
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Hi is it possible to run MM/GBSA? Or any suggestions on how after simulation?
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Dear Dr. Yadav. Thank you for your precious video for DM simulation. Please be noted, I will send you an email to show you some details.
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Thank you for video.
Thank you very much! I am glad that you like it.
Please feel free to contact me in the future!
All the best!
Ma'am, I have a question. Can we use this portal for MD simulation of Protein-protein docked structure? I have the pdb file of the docked molecule and want to do the simulation part only. Is that possible?
Yes it’s possible!
Please give it a try!
Thank you 💜
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Maam, if ligand weight is more than 400...what can I do
If the ligand weight is more than 400, you can't perform the docking or simulation on myPresto portal. You have to either purchase the paid version GUI Moldesk (www.moldesk.com/) or use free CLI myPresto software (www.mypresto5.jp/en/).
Please feel free to contact me in the future!
All the best!
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
I'm facing a problem while doing MD. function limitation of free version no. of atoms=106479>25000. Can you help me in solving this?
If the number of atoms is more than 25000, you can't perform the docking or simulation on myPresto portal. You have to either purchase the paid version GUI Moldesk (www.moldesk.com/) or use free CLI myPresto software (www.mypresto5.jp/en/).
Please feel free to contact me in the future!
All the best!
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
Can you please let us know how to get RMSD and RMF using VMD using MyPresto generated files!
Thank you!!!
In myPresto Portal, after selecting your protein or ligand or both, go to "File" and select "Export PDB". This will export trajectory in PDB format and then you can open it in VMD.
After opening PDB file in VMD, go to "Extensions", go to "Analysis", then select "RMSD Calculator", "RMSD Trajectory Tool", or "RMSD Visualizer Tool" to check RMSD.
If you have any queries, please ask the experts on this link. They will respond to you ASAP. www.mypresto5.jp/en/contact/
How much is the paid version ma'am?
You have to contact Moldesk (www.moldesk.com/) to know the price.
Please feel free to contact me in the future!
All the best!