I had run MD simulation with NAMD and want to check the differences of R of G during the simulation time. Is it important and efficient to record R of G? or there is another parameter that I should calculate?
Thanks
Abdo
Radius of gyration is going to give you distribution of atoms of protein around a certain axis. In this context, it has been used to distinguish between an folded alpha helical structure and an unfolded one, or between alpha helical structure and beta sheet structure. For a (complex) protein structure with alpha helical and beta sheets, it may be difficult to interpret values of R of G, however, you may use it to analyze folded structure of parts of your protein.
Thanks, Petar Žuvela
I have followed the tutorial but it just calculates the R of G of the last frame of the loaded DCD file.
Thanks, Hiqmet Kamberaj
But if the folding is not changed; just movement of part of the protein relative to the rest of the protein (arm movement). How can we benefit from R of G?
I have made a sample tcl script to loop through dcd file to output a .dat file which contains radius of gyration of the protein in each frame. Also attaching other necessary tcl files. Run rog_loop_dcd.tcl keeping other tcl files in the same folder and replace the dcd and psf file locations with your ones. Thank you. Please reply if you find any mistake or trouble. I don't know if it is an efficient program. But it does the job.
Dear Devanand
I have run your modified script and it is working good with VMD (no clashes occurred).
Thank you my friend and I will not forgive your kind help :)
Can you post the modified script here for reference?
See you
Abdo
So the rog_loop_dcd.tcl I uploaded before had a minor issue. I am updating the code here based on Abdo's reply. I am happy if this helped you. (I have updated the code above also. The changes are given below)
source gyr_radius.tcl
source center_of_mass.tcl
set outfile [open radius_of_gyration.dat w]
puts $outfile "i rad_of_gyr"
set nf [molinfo top get numframes]
set i 0
set prot [atomselect top "protein"]
while {$i < $nf} {
$prot frame $i
$prot update
set i [expr {$i + 1}]
set rog [gyr_radius $prot]
puts $outfile "$i $rog"
}
close $outfile
Dear Devanand T Santha Sir,
I run the file provided by you for the radius of gyration prediction, but i didn't get any output. Kindly help me out.
I saved the all .tcl file in the folder where all the simulation files are saved.
i am getting
Unable to load file '/home/devanandt/Documents/RAS/model/DATA/model/ANALYSIS/fitted_DCD/APO/model_APO_RAS_200ns_fitted.psf' using file type 'psf'.
error. Kindly help.
Give your psf file. And the correct location to your file in the system. This example file is from my computer
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