VMD-L Mailing List

From: Alberto Sergio Garay (sgaray_at_fbcb.unl.edu.ar)
Date: Thu Nov 18 2010 - 07:12:46 CST

Hi all

I'm running a tcl script to calculate a frequency of thymine piling up
during a MD simulation. When I load the trajectory in VMD (graphical
mode) and then run the script, everything is OK, but when I try to run
vmd without open the graphical environment, the trajectory starts to
be loaded, but after some time, it gives me the message: killed.

my script includes the directive waitfor all

Could anyone give a clue about this problem? What am I doing wrong?
Why the script works well under the graphical environment and not in
command line?

Below I paste the script

mol new run_completo.gro
mol addfile run_completo.xtc steps 1 waitfor all

#Enter the name for the output file
set filename1 "file_out.dat"

#Distance cutoff between thymine rings
set dist_cutoff 5.0

set PI 3.14159265358979

#Angle between normal vectors of close (within dist_cutoff distance)
thymine rings
set angle_cutoff 20.0

#Extract frames from file
set num_steps [expr [molinfo top get numframes] - 1]

#Open files for writing
set out [open $filename1 w]

#Making an array of list of resids
for {set j 1} {$j <= 16} {incr j} {
        set r($j) {}
        set Center($j) 0.0
        #array over each atom selected
        for {set k 1} {$k <=4} {incr k} {
                set at($j,$k) {}
        }
}

#Making an array of residues' piling ups
for {set i 1} {$i <= 16} {incr i} {
        for {set j 1} {$j <= 16} {incr j} {
                set Pile($i,$j) 0
        }
}

#Making selections
set sel1 [atomselect top "resid 2 4 6 8 10 12 14 16 18 20 22 24 26 28
30 32 and name CT2 NT1 NT2 CT5"]

for {set frame 1} {$frame <= $num_steps} {incr frame} {
$sel1 frame $frame
$sel1 update

puts "frame: $frame"

#making a list of at. names and coordinates
set at_names [$sel1 get name]
set coords [$sel1 get {x y z}]

        for {set i 1} {$i <= 16} {incr i} {
                #Assign the first 4 elements of the list to a residue
                set r($i) [lrange $coords 0 3]
                #then delete the 4 first elements of the list
                set coords [lreplace $coords 0 3]
                #summing over resids
                set Sum {0 0 0}
                set at_idx 0
                foreach b $r($i) {
                        set at_idx [expr $at_idx + 1]
                        set Sum [vecadd $Sum $b]
                        set at($i,$at_idx) $b
                }
                set Center($i) [vecscale [expr 1.0 / 4] $Sum]
                #puts "Center($i): $Center($i)"
        }

        for {set i 1} {$i <= 16} {incr i} {
                for {set j 16} {$j > $i} {incr j -1} {
                        set dist [veclength [vecsub $Center($i) $Center($j)]]
                        if {$dist <= $dist_cutoff} {
                                puts "dist: $dist"
                                set v1 [vecnorm [vecsub $at($i,1) $at($i,2)]]

                                set v2 [vecnorm [vecsub $at($i,3) $at($i,2)]]
                                set N1 [veccross $v1 $v2]

                                ####################################
                                set v3 [vecnorm [vecsub $at($j,1) $at($j,2)]]
                                set v4 [vecnorm [vecsub $at($j,3) $at($j,2)]]
                                set N2 [veccross $v3 $v4]

                                ######################################
                                set angle [expr 180 - (acos([vecdot $N1 $N2]) * 180 / $PI)]
                                puts "angle: $angle"
                                if {$angle <= $angle_cutoff} {
                                        set Pile($i,$j) [expr $Pile($i,$j) + 1.0]
                                        puts "Pile($i,$j): $Pile($i,$j)"
                                }
                                if {$angle >= [expr 180 -$angle_cutoff]} {
                                        set Pile($i,$j) [expr $Pile($i,$j) + 1.0]
                                        puts "Pile($i,$j): $Pile($i,$j)"
                                }
                        }
                }
        }
}
#Normalizing by the number of frames
#Making an array of residues' piling ups
for {set i 1} {$i <= 16} {incr i} {
        for {set j 1} {$j <= 16} {incr j} {
                #puts "Pile($i,$j): $Pile($i,$j) --> num_steps: $num_steps"
                set Pile($i,$j) [expr ($Pile($i,$j) * 1.0) / $num_steps]
                puts "Pile($i,$j) after normalization: $Pile($i,$j)"
        }
}
#writing the matrix of interations
for {set j 1} {$j <= 16} {incr j} {
puts $out "$Pile($j,1) $Pile($j,2) $Pile($j,3) $Pile($j,4) $Pile($j,5)
$Pile($j,6) $Pile($j,7) $Pile($j,8) $Pile($j,9) $Pile($j,10)
$Pile($j,11) $Pile($j,12) $Pile($j,13) $Pile($j,14) $Pile($j,15)
$Pile($j,16)"
}
close $out
quit

Thank you in advance.

Sergio 

-- 
Dr. Sergio Garay
Facultad de Bioquimica y Cs. Biológicas
Universidad Nacional del Litoral
Santa Fe - Argentina
C.C. 242 - Ciudad Universitaria - C.P. S3000ZAA
Argentina
Ph. +54 (342) 4575-213
Fax. +54 (342) 4575-221