Hey Guys,
I have a ubiquitin,
I am planning to claculate radius of gyration for residue 1 to 24 and 25 to 76.
How can I make this?
What command shall I use?
Thank you.
Maryam
You can calculate the Radius of gyrations of the selected amino acids using the Tcl script below in VMD. Import the residue names in the **atomselect top " (protein and resid 149)*** (For example, this is for the residue No. 149 from the protein residues)
set mol [molinfo top]
set out [open HB.dat w]
set sel [atomselect top " (protein and resid 149) and backbone "]
set frames [molinfo $mol get numframes]
for {set i 0} {$i < $frames} {incr i} {
$sel frame $i
$sel update
puts $out "$i [measure rgyr $sel]"
}
$sel delete
Hi Ramin.
Thank you very much for your comment,
I followed it and I got error in here:
puts $out "$i [measure rgyr $sel]"
It says: no such variable.
Besides, I want to tell VMD, please calculate Rg for residues 1 to 72.
How can I write it in here?
(protein and resid 149) and backbone "]
Maryam :)
Hi Maryam,
This command will select the residues 1 to 72:
set sel [atomselect top " (protein and resid 1 to 72) and backbone "]
I prepared a tcl file, that is rgy.tcl, please find attached. Go to "extensions >Tk console" of VMD and then run the script by: $source rgy.tck
It will work and generate a file, that is HB.dat, including the results.
hope it's helpful,
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