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From: Ricard Argelaguet (ricard.argelaguet_at_gmail.com)
Date: Thu May 29 2014 - 11:22:18 CDT
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I need to calculate the RMSF for all CA atoms for 500 trajectories, so I
need to automatize the computation.
I have the following script:
proc rmsf_all_ca {} {
set file_name "Calfa-rmsf.dat"
set outfile [open $file_name w];
set sel [atomselect top "resid 1 to 198 and name CA"]
set mol [$sel molindex]
for {set i 0} {$i < [$sel num]} {incr i} {
set rmsf [measure rmsf $sel]
puts $outfile "[expr {$i+1}] [lindex $rmsf $i]"
}
close $outfile
}
However, I am encountering the following problem: In order to calculate
RMSF, I need to align first, and I usually do it manually with the VMDTT.
But now I have to automatize that step. I know about the use of measure fit
to align and calculate RMSD. However, for RMSF is more complicated as I do
not have a single reference frame.
Any idea??
Thanks!
- Next message: Axel Kohlmeyer: "Re: Calculating RMSF for a lot of trajectories"
- Previous message: Josh Vermaas: "Re: psfgen-reading residues above 10 thousand"
- Next in thread: Axel Kohlmeyer: "Re: Calculating RMSF for a lot of trajectories"
- Reply: Axel Kohlmeyer: "Re: Calculating RMSF for a lot of trajectories"
- Reply: Josh Vermaas: "Re: Calculating RMSF for a lot of trajectories"
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