From: yp sun (sunyeping_at_yahoo.com.cn)
Date: Thu Oct 04 2012 - 04:43:37 CDT
Dear all,
I want to analyze the NAMD simulation results, especially RMSD during the time. But it is difficult for me to understand the tcl script. The following is a tcl script from NAMD-tutorial for computing rmsd of each residue during the timesteps:
proc rmsd_residue_over_time {{mol top} res} {
# use frame 0 for the reference
set reference [atomselect $mol "protein" frame 0]
# the frame being compared
set compare [atomselect $mol "protein"]
#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 $filI
}
Could you explain in detail what are the functions of every stentences? For example, what role is the following loop sentence for?
" foreach r $res {
set rmsd($r) 0
}"
My simulation is done on a protein containing three chains. I feel this script is not suitable for calculation every residue in individual chains. Then how should I modify it? Thanks
Best regards!
Yeping Sun
CAS Key Laboratory of Pathogenic Microbiology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
This archive was generated by hypermail 2.1.6 : Tue Dec 31 2013 - 23:22:39 CST