Can you tell me how can we add two heme residues for selection?. I tried sel protein and chain HETA and HETB did not work. Perhaps needs to select other atoms from the heme group. because in your script, I see only alpha carbons
Hey Mohamed, Great tutorial and tbh the only one on youtube regarding RMSF. Your script seems to work fine when I'm using a single protein (yielding 230 RMSD's for each of the 230 residues) - but when I'm using it for my protein-ligand complex, its somehow yielding 240 RMSDs. I am assuming that maybe the CA atoms of my ligand is also being considered hence the 10 extra RMSDs. Do you know whether its the first 10 or the last 10 RMSDs of the list that would belong to the ligand? In my complex's psf file, the ligand has a separate chain name (chain B) than my protein (chain C) and is after the protein sequence. Also, the ligand's resid is 1, my protein starts with a resid 16.
Hi, you adjusted your atom selection according to your structure , since I had only protein I set my sel as protein but in your case you should choose only protein without ligand.. for example you say "protein and resid 16 to 230... this will give you only the RMSF of your protein without the legend or you could keep it protein and remove the first 10 RMSFs from your output file but this would be very stupid so as I said it is better to modify your script to selsect only proteins residues .. I advice you to go over the atomselect command usage in VMD tutorials
Great work Shehata. I have a question. Actually, I am also doing the simulation using the quick MD plugin into VMD and NAMD software. After running the simulation, my protein comes out from the box. How can we remove this problem? I am looking forward to you and thanks in advance.
@@Mohamedshehata Thanks a lot for your reply. Hope you are doing well in this challenging time. Again, my concern is, we are using the wrap command after the simulation is done. So do you think there will be a change in the energy of the system?
thank you but can you suggest program to get good figures of RMSD and RMSF ? Also if I want to calculate rmsf for my protein ligand complex what should I write in the selected atoms?
How can I get the RMSF per residue, it seems here that the RMSF values is per/atom, I tried the script several times with different selections and it gives per atom information
It is clear in the script that I selected " protein and CA" because one should be interested in the fluctuations of the backbone. SO RMSF1 means the fluctuation of the CA of res1. If you want all atoms you can change this selection to " protein" and it will calculate for all the atoms. But the data will become very noisy because the side chain fluctuations are somehow meaningless.
set reference [atomselect top "protein" frame 1] # the frame being compared set compare [atomselect top "protein"] set num_steps [molinfo top get numframes] for {set frame 0} {$frame < $num_steps} {incr frame} { # get the correct frame $compare frame $frame # compute the transformation set trans_mat [measure fit $compare $reference] # do the alignment $compare move $trans_mat } set outfile [open RMSF.txt w] set sel [atomselect top "name CA"] #puts $outfile "[measure rmsf $sel first 1 last 2000 step 1]" set rmsf [measure rmsf $sel first 0 last 4999 step 1] for {set i 0} {$i < [$sel num]} {incr i} { puts $outfile "[expr {$i+1}] [lindex $rmsf $i]" } close $outfile
Hello, it was really useful. I have a query: How can I calculate the RMSF for each residue of dsDNA?
hi, where i can get the script for the rmsf measurement? just like what u used, please the link. Thanks.
Can you tell me how can we add two heme residues for selection?. I tried sel protein and chain HETA and HETB did not work. Perhaps needs to select other atoms from the heme group. because in your script, I see only alpha carbons
Thanks. Am working with a nucleosome. How can I plot the RMSF of the nucleic acid alone?
Sir am working with protein peptide how can I plot eagenvalue for complex structure
Thanks sir shehata, plz how we can analyze the interactions Lig-Prot after MD simulation.
Hey Mohamed, Great tutorial and tbh the only one on youtube regarding RMSF.
Your script seems to work fine when I'm using a single protein (yielding 230 RMSD's for each of the 230 residues) - but when I'm using it for my protein-ligand complex, its somehow yielding 240 RMSDs. I am assuming that maybe the CA atoms of my ligand is also being considered hence the 10 extra RMSDs. Do you know whether its the first 10 or the last 10 RMSDs of the list that would belong to the ligand? In my complex's psf file, the ligand has a separate chain name (chain B) than my protein (chain C) and is after the protein sequence. Also, the ligand's resid is 1, my protein starts with a resid 16.
Hi, you adjusted your atom selection according to your structure , since I had only protein I set my sel as protein but in your case you should choose only protein without ligand.. for example you say "protein and resid 16 to 230... this will give you only the RMSF of your protein without the legend or you could keep it protein and remove the first 10 RMSFs from your output file but this would be very stupid so as I said it is better to modify your script to selsect only proteins residues .. I advice you to go over the atomselect command usage in VMD tutorials
what did you write in the selected atoms for your protein ligand complex?
can you send me the script you used?
Hello. What would you do recommend if my .dcd file is 30 Gb ? I cannot load it into VMD 'cause it keeps crashing the software...
if you don't need all the frames load with stride 10 or more
Great work Shehata.
I have a question. Actually, I am also doing the simulation using the quick MD plugin into VMD and NAMD software. After running the simulation, my protein comes out from the box. How can we remove this problem? I am looking forward to you and thanks in advance.
That's a PBC issue. I have a video in my channel explain how to handle it please refer to it
@@Mohamedshehata Thanks a lot for your reply. Hope you are doing well in this challenging time. Again, my concern is, we are using the wrap command after the simulation is done. So do you think there will be a change in the energy of the system?
@@gauravkumarbhali514 Wrap is just handling visualization of the system it doesn't change anything else , don't worry
can you please suggest script using crystal (or pdb structure/energy minimized structure) as the reference for rmsf and rmsd?
thank you but can you suggest program to get good figures of RMSD and RMSF ? Also if I want to calculate rmsf for my protein ligand complex what should I write in the selected atoms?
@@punctdan Thank you so much I will do it.
Thanks. Please, Upload a video on free energy calculation by VMD.
Soon!!
Thank you much, Your teaching is superb. Please, sir, can you make a video on how to install cafe1.0 for windows 10.
How can I get the RMSF per residue, it seems here that the RMSF values is per/atom, I tried the script several times with different selections and it gives per atom information
It is clear in the script that I selected " protein and CA" because one should be interested in the fluctuations of the backbone. SO RMSF1 means the fluctuation of the CA of res1. If you want all atoms you can change this selection to " protein" and it will calculate for all the atoms. But the data will become very noisy because the side chain fluctuations are somehow meaningless.
@@Mohamedshehata Thank you very much for the explanation
@@ahmadalqaisi9828 you are always welcome bro !
Thank you. Could you please share a reference to cite?
to cite what? VMD ?
set reference [atomselect top "protein" frame 1]
# the frame being compared
set compare [atomselect top "protein"]
set num_steps [molinfo top get numframes]
for {set frame 0} {$frame < $num_steps} {incr frame} {
# get the correct frame
$compare frame $frame
# compute the transformation
set trans_mat [measure fit $compare $reference]
# do the alignment
$compare move $trans_mat
}
set outfile [open RMSF.txt w]
set sel [atomselect top "name CA"]
#puts $outfile "[measure rmsf $sel first 1 last 2000 step 1]"
set rmsf [measure rmsf $sel first 0 last 4999 step 1]
for {set i 0} {$i < [$sel num]} {incr i} {
puts $outfile "[expr {$i+1}] [lindex $rmsf $i]"
}
close $outfile
ty mate
how to do Radius of Gyration (RoG),
there is already video in my channel about it
How can we calculate RMSF and RMSD for a particular chain in a protein ?
In your selection , instead of saying protein , say " protein and chain ID" for example " protein and chain A.
Good luck !