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
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
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
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?
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?
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.
