VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Feb 16 2021 - 05:12:14 CST

your script most likely has a memory leak through creating atom selections
inside a loop and not deleting them.
axel.

On Tue, Feb 16, 2021 at 6:05 AM Sunita Patel <sunita.patel_at_cbs.ac.in> wrote:

> Dear VMD-users,
>
> I wrote a tcl script to find the number of native contacts in each frame.
> The reference frame (frame 0) whose native contacts have been matched with
> other frames. This program is working fine with a small number of frames
> (frames 30). However it crashed when I ran the program for 400 frames.
>
> I need your help to rectify the program so that it will work for a larger
> number of frames. Please find the program appended below or also as an
> attachment.
>
> Your help will be highly appreciated.
>
> Sincerely,
> Sunita
> ============================================================
> # Usage "source vmd_native_contacts.tcl" source vmd_native_contact 0.
> # First frame is considered as reference native structure.
> proc vmd_native_contacts { mol } {
> puts "Enter output file name:"
> set outputfilename [gets stdin]
> set output [open $outputfilename w]
>
> set allCa [atomselect $mol "name CA"]
> #get the index of CA atoms
> set rid [$allCa get index]
> # No. of C-alphas
> set ridLength [llength $rid]
> set num [molinfo $mol get numframes]
> set k 0 ;
> set allcontacts {}
> # Iteration over frames
> while {$k < $num} {
> set ctr 0
> set contactCa {}
> #compare the CA atoms pair which are separated by 6.5 Ang or less
> for {set i 0} {$i < $ridLength} {incr i} {
> for {set j [expr $i+4]} {$j < $ridLength} {incr j} {
> set fir [lindex $rid $i];
> set sec [lindex $rid $j];
> set firNdx [atomselect $mol "index $fir" frame $k];
> set secNdx [atomselect $mol "index $sec" frame $k];
> set firCen [measure center $firNdx];
> set secCen [measure center $secNdx];
> set diff [vecsub $firCen $secCen];
> set dist [veclength $diff];
> if {$dist < 6.5} {
> set ctr [expr $ctr + 1]
> lappend contactCa "$fir $sec" ;
> }
> }
> }
> # CA-atomd distance less than 6.5 are put in the list 'allcontacts'.
> lappend allcontacts "$contactCa" ;
> set k [expr $k + 1]
> }
>
> # No. of native contacts in the reference structure that is 'frame 0'.
> set nrefNc [llength [lindex $allcontacts 0]];
> # No. of frames 'fr'.
> set fr [llength [lindex $allcontacts]];
> # Searching of native contacts from frame 1 onwards (frame 0 is the
> reference)
> for {set m 1} {$m < $fr} {incr m} {
> set Ncontact 0
> for {set n 0} {$n < $nrefNc} {incr n} {
> set refNc [lindex $allcontacts 0 $n];
> set search [lsearch [lindex $allcontacts $m] "$refNc"]
> if {$search != -1} {
> set Ncontact [expr $Ncontact + 1]
> }
> }
> set pcgNC [expr ([format %8.1f $Ncontact] / [format %8.1f $nrefNc]) * 100]
> puts $output "$m [format %8.1f $pcgNC]";
> flush $output;
> }
> }
> ====================================================
>
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  https://urldefense.com/v3/__http://goo.gl/1wk0__;!!DZ3fjg!omCy0XGQfONdQYOAoqjnjJ4VFXPDEcxW5vWLWxMeymRsSpj7nYDUj-h0w6i1rGXEZw$ 
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.