I ran a MD simulation for a protein with a ligand, and I would like to calculate the RMSF for each residue. Are there any scripts for this?
It is possible to calculate RMSF using VMD or VMD/tcl script. The following links might be helpful:
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/23817.html
https://www-s.ks.uiuc.edu/Training/Tutorials/science/timeline/tutorial_timeline-html/node4.html
Thank you very much Anagana and Lada. Your links were very helpful and informative.
Use VMD.
The following script should do the job:
#$Id: residue_rmsd.tcl,v 1.4 2006/03/06 23:56:46 timisgro Exp $
proc rmsd_residue_over_time {{mol top} res } {
# use frame 0 for the reference
set reference [atomselect $mol "protein and alpha" frame 0]
# the frame being compared
set compare [atomselect $mol "protein and alpha"]
#make a selection with all atoms
set all [atomselect top all]
#get the number of frames
set num_steps [molinfo $mol get numframes]
#open file for writing
set fil [open residue_rmsd.dat w]
foreach r $res {
set rmsd($r) 0
}
#loop over all frames in the trajectory
for {set frame 0} {$frame < $num_steps} {incr frame} {
puts "Calculating rmsd for frame $frame ..."
# get the correct frame
$compare frame $frame
$all frame $frame
# compute the transformation
set trans_mat [measure fit $compare $reference]
# do the alignment
$all move $trans_mat
# compute the RMSD
#loop through all residues
foreach r $res {
set ref [atomselect $mol "protein and resid $r and noh" frame 0]
set comp [atomselect $mol "protein and resid $r and noh" frame $frame]
set rmsd($r) [expr $rmsd($r) + [measure rmsd $comp $ref]]
$comp delete
$ref delete
}
}
set ave 0
foreach r $res {
set rmsd($r) [expr $rmsd($r)/$num_steps]
# print the RMSD
puts "RMSD of residue $r is $rmsd($r)"
puts $fil " $r \t $rmsd($r)"
set res_b [atomselect $mol "resid $r"]
$res_b set user $rmsd($r)
$res_b delete
set ave [expr $ave + $rmsd($r)]
}
set ave [expr $ave/[llength $res]]
puts " Average rmsd per residue: $ave"
close $fil
}
All the best.
Inn case this is still an issue, in vmd there is the timeline tool. That has the calculate RMSF function.
There are 2 VMD tcl scripts here, one for calculating protein RMSF and one for nucleic acid.
Hi:
I recommend the vmd plugin called vmdICE From here you will download the manual and the necessary files to connect it to the visual interface of VMD
http://www.meduniwien.ac.at/msi/biosim/bk/a1375/
regards
IN VMD toolbar
Extensions > Analysis > timeline > calculate > calc. RMSF
Hi Shashank Chavali:
In VMD:
1) First, align your sistem (for example with RMSD_Visualizer Tool or some script with measure fit).
2) Go to Tk Console (Extensions-Tk Console) and use the following script :
set fp [open "rmsf.dat" w] set sel [atomselect top "protein and name CA"] for {set i 0} {$i < [$sel num]} {incr i} { set rmsf [measure rmsf $sel first 1 last 4999 step 10] puts $fp "[expr {$i+1}] [lindex $rmsf $i]" } close $fp
In this example, the script will calculate the RMSF of all CA atoms from frame 1 to 4999.
Note: residues will apear from number 1 (correlative order)
Ignacio Lizana
my friend, please tell me what is the meaning of fp in this Tcl code?
the tk console says: can't read "fp": no such variable
what should I do?
best regards
Soroush Ziaei:
"fp" is only the name of the first variable and is used to export the rmsf data with the code "[open "rmsf.dat" w]". May be your problem is a copy-paste mistake. You can download the following script attached (rmsf_script.txt). Copy all content of the script in the VMD TkConsole and then press ENTER when it shows "close $fp".
Regards
Ignacio Lizana How can I calculate RMSD regarding the previous time frame as a reference? I mean the ref frame is not the frame 0 it is the last one for each frame.
Roya Jafari Sorry, but I really don't know how to write that kind of script.
Ignacio Lizana How to plot the RMSD values as Å vs ns not as Å vs frame?
Thanks
Apu Chowdhury
First, convert frame to nanosecond in your file and then plot RMSD vs ns.
Regards
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