VMD-L Mailing List

From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Fri Apr 25 2014 - 01:13:38 CDT

Doesn’t „measure Hbonds“ also need the hydrogens, as the angle is measured D->A->H? Also I’m not sure if “N.*” works, why not simply use “nitrogen or oxygen or hydrogen”. The HBonds drawing method does work with only the heavy atoms selected, but maybe not so the measure command.

 

Norman Geist.

 

Von: owner-vmd-l_at_ks.uiuc.edu [mailto:owner-vmd-l_at_ks.uiuc.edu] Im Auftrag von HongTham
Gesendet: Freitag, 25. April 2014 02:52
An: vmd-l_at_ks.uiuc.edu
Betreff: vmd-l: measure Hbond and orient (with vec {0 0 1}) of a selected molecule

 

Hi VMD users,

I have some problem in calculating Hydrogen bond and orient that I cant resolve them. Thanks in advance for any advices

1. Measure Hbond:

I made the Tcl script below. although in visual simulation there are some hbonds, and by TC console as well, the file out just display {} {} {}. I set cutoff 3.4 and angle 30.

mol new ../proion.pdb
animate delete all
mol addfile ../pro12_16.dcd waitfor all
mol addfile ../pro17_31.dcd waitfor all
mol addfile ../pro32_46.dcd waitfor all
mol addfile ../pro47_61.dcd waitfor all
mol addfile ../pro62_76.dcd waitfor all
mol addfile ../pro77_89.dcd waitfor all
mol addfile ../pro90_99.dcd waitfor all

source /home/hongtham/VMD/Nhbond.tcl

set nf [molinfo 0 get numframes]
set clist [list A C D]

foreach ch $clist {
    set fout [open "hbond$ch.dat" w]
    set sel [atomselect 0 {protein and chain $ch and resid 180 to 200 and name "N.*" "O.*"}]

#calculation
    for { set i 0 } { $i < $nf } { incr i } {
        $sel frame $i

        puts $fout "[expr ($i*0.01)+20.1] [Nhbond $sel]"
    }
    close $fout
}
~

the source script is below:
# Count the number of H-bonds with one selection

proc Nhbond {sel {cutoff 3.4} {angle 30}} {
    return [measure hbonds 3.4 30 $sel]
}

       

2. measure orient

with the same selected molecule. I made the script below, i try to find some explaination about the script but file out has nothing. Thank for any suggestion

# analysis
    set clist [list A B C D E]
    set vec {0 0 1}
#set clist [list A ]
   # set fout [open "ori$ch.dat" w]

foreach ch $clist {
    set fout [open "ori$ch.dat" w]
    set sel [atomselect 0 "protein and chain $ch and name CA"]
    set fout [open "ori$ch.dat" w]

# distance calculaton
      for { set i 0 } { $i < $nf } { incr i } {
         $sel frame $i
      
 set ori [orient $sel $vec]
        puts $fout "$ori"
    }
    close $fout

and the source script is:
proc orient { sel {vec {0 0 1} }} {
    set all [atomselect [$sel molid] "all"]
    set vec [vecnorm $vec]

    set vec1 [lindex [measure inertia $sel] 1 2]
    set vec2 [vecnorm [veccross $vec1 $vec]]
    set ang [expr acos([vecdot $vec1 $vec])]
    $all move [trans center [measure center $sel] axis $vec2 $ang rad]
}

Thank you so much.

Hong Tham

Biomedical engineering department

Pukyong National University

Pusan, South Korea

email: hongtham0709_at_gmail.com

  

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