Excellent tutorial, thanks. But I get the error message "must have at least one atom in selection". Baffling really....I followed your video exactly. Look forward to your comments.
Thank you so much for this, will acknowledge you in my University dissertation as thank you, have not been able to find anything else to help me with this fo my honours project Great video my guy
Thank you so much for the tutorial! If you allow me to ask, how do you convert the frame to second? I used VMD (namd2) with the standard protocol, and the rg.dat file gives me the frame versus radius. How can I convert to time versus radius? Thanks!
Thank you very much for the great video! Currently, I am also learning this. Do you have any suggestion on simulating the interaction of a molecule with the lipid bilayer with different composition (different ratio of POPC:POPE)? Thank you!
Thank you for the excellent video. Just a query: proteins tend to rely on hydrophobic interaction a lot to maintain its 3D structure. However, in a organic solvent due to absence of this don't you think the protein will unfold/misfold and hence have lesser stability.
Which solvent we are talking about here? polar or no polar ? and which enzymes ? it is not a general effect.. Kindly refer to one of my papers explains this in details ..good luck link.springer.com/article/10.1007/s00894-020-04396-3
@@Mohamedshehata yah... I went through that a long back.... if you tell about how to interpreet the sasa results it will be so helpful.... suppose for a protein-ligand system, if sasa value increased or decreased or remain same when compare with the apo protein sasa value what it indicates?
Excellent tutorial, thanks. But I get the error message "must have at least one atom in selection". Baffling really....I followed your video exactly. Look forward to your comments.
@@Mohamedshehata Hello Mohamed, thanks for your prompt reply. Yes, my PhD is based around nucleic acids. I wondered if the problem lies with NAMD autopsf_builder. But using psfgen doesn't make a difference. I have successfully applied all other metrics to the DNA model I'm investigating...rmsd etc. I'm using toppar files relevant to nucleic acids. I suspect it will be a simple solution to this Rg problem, but after 5 days...I can't figure it out. Look forward to your comments
@@simonfox3220 Hi Simon! As I guessed you are not simulating a protein that's why you are getting this error "'no atoms selected" you should modify my script from [atomselect top "protein"] to whatever you are simulating. Say your system is a simulation of ice cream with vanilla and chocolate. You can change it to [atomselect top "all"] or if you want to compute Rg only for part of the system say vanilla, you can say "[atomselect top "ice cream and not chocolate "] or [atomselect top "ice cream and vanilla"] and so on :)
@@Mohamedshehata Hello Mohamed. Yes, that worked, many thanks. I used "all" and "nucleic" in the rog_loop_dcd.tcl file. Both work, but the latter gives slightly lower values. Which is a bit of a surprise because NAMD Rg should be measuring the same number of atoms? Anyway, thanks again, hope I can return the favour one day!
Scripts are in the video description
Excellent tutorial, thanks. But I get the error message "must have at least one atom in selection". Baffling really....I followed your video exactly. Look forward to your comments.
If any one needs the scripts that I used in this video please write your email in a comment and I will send it to you .. Good luck
Please can you send the scripts to me
@@Ahmed87810 could you write your eamil?
@@Mohamedshehata I send Email to you
@@Ahmed87810 Sent , good luck !
@@Mohamedshehata Hi can you please send me the scripts? montesc.ruben@gmail.com
Hello sir
Whenever i run the code, vmd stops working
What could be the reason?
Thank you so much Mohamed! We appreciate your efforts. These tutorials are gem for a beginner like me.
Happy to hear that :) keep it up !
What are the units of Radius of Gyration calculated in this way?
Thank you so much for this, will acknowledge you in my University dissertation as thank you, have not been able to find anything else to help me with this fo my honours project
Great video my guy
Good luck Liam Would be happy to see a screenshot of the acknowledgement just to show off hehehe
Thanks a lot sir. Your videos and scripts are really helpful for me.
Good luck!
Great work here!
Thank you!
Does the loop compute the center of mass using the mass and position of every atom (or every amino acid or subunit? ) in the system per frame?
Thank you so much for the tutorial! If you allow me to ask, how do you convert the frame to second? I used VMD (namd2) with the standard protocol, and the rg.dat file gives me the frame versus radius. How can I convert to time versus radius? Thanks!
How can i get the graph of rg vs nanoseconds? Please help me in this regards. I'm a subscriber of your channel
import your results to python and plot it with matplotlib ..chatgpt can help you do it easily
Thank you very much for the great video!
Currently, I am also learning this. Do you have any suggestion on simulating the interaction of a molecule with the lipid bilayer with different composition (different ratio of POPC:POPE)? Thank you!
wonderful video, thank you so much
very inforamtive
Scripts are in the video description
thanks!
Is it possible to use python scripts instead of tcl
Thank you for the excellent video. Just a query: proteins tend to rely on hydrophobic interaction a lot to maintain its 3D structure. However, in a organic solvent due to absence of this don't you think the protein will unfold/misfold and hence have lesser stability.
Which solvent we are talking about here? polar or no polar ? and which enzymes ? it is not a general effect.. Kindly refer to one of my papers explains this in details ..good luck link.springer.com/article/10.1007/s00894-020-04396-3
Can you please tell how you generated theseplots after having data in text form?
you can use python or any plotting tools
can u plz tell us about SASA, DSSP, and PCA analysis?
SASA is already in my channel
@@Mohamedshehata yah... I went through that a long back.... if you tell about how to interpreet the sasa results it will be so helpful.... suppose for a protein-ligand system, if sasa value increased or decreased or remain same when compare with the apo protein sasa value what it indicates?
@@debanjansen1282 you need to read papers to understand what you want
Thank you very much for for this useful video.
pls can you help me how can i do programming with MOLPRO
You are welceom!
I don't know it
Excellent tutorial, thanks. But I get the error message "must have at least one atom in selection". Baffling really....I followed your video exactly. Look forward to your comments.
I guess you are not measuring Rg for protein ? right ?
@@Mohamedshehata Hello Mohamed, thanks for your prompt reply. Yes, my PhD is based around nucleic acids. I wondered if the problem lies with NAMD autopsf_builder. But using psfgen doesn't make a difference. I have successfully applied all other metrics to the DNA model I'm investigating...rmsd etc. I'm using toppar files relevant to nucleic acids. I suspect it will be a simple solution to this Rg problem, but after 5 days...I can't figure it out. Look forward to your comments
@@simonfox3220 Hi Simon! As I guessed you are not simulating a protein that's why you are getting this error "'no atoms selected"
you should modify my script from [atomselect top "protein"] to whatever you are simulating. Say your system is a simulation of ice cream with vanilla and chocolate. You can change it to [atomselect top "all"] or if you want to compute Rg only for part of the system say vanilla, you can say "[atomselect top "ice cream and not chocolate "] or [atomselect top "ice cream and vanilla"] and so on :)
@@Mohamedshehata Hello Mohamed. Yes, that worked, many thanks. I used "all" and "nucleic" in the rog_loop_dcd.tcl file. Both work, but the latter gives slightly lower values. Which is a bit of a surprise because NAMD Rg should be measuring the same number of atoms? Anyway, thanks again, hope I can return the favour one day!
much late but if anyone has the same issue. Its because you have selected wrongly using the atomselect. First test your atom selections in Tk console