VMD-L Mailing List

From: Alberto Sergio Garay (sgaray_at_fbcb.unl.edu.ar)
Date: Tue Jun 30 2009 - 12:08:32 CDT

Dear Axel

First, I want to apology for my spelling mistakes! I am really sorry!.
I wrote the previous mail very fast, but from now I will do it carefully.

Second, below I paste the script again, with your strong suggestion
included. The problem is still the same, so I am also pasting the same
writing which I sent in the previous mail:

> I'm running a script which selects some particular residue and wraps
> the rest >of the atoms around it.
> After that the script selects some residues and some water molecules
> to look or >hBonds between them. The script informs that there were
> not any hbonds between >this two selections. I checked visually that
> the selected residues were >corrects i.e. all the atoms selected
> were close each other. The strange is when >I select the residues
> (previously wrote down by my tcl/tk script) in the tcl/tk >window
> and run hbonds measure I can find the hbonds, which I hoped.
>
> Could any one give any clue of what I'am doing wrong?

Thank you in advance.

#Please, enter the residue to use for the centre of the calculation
set resid 60
#Enter the radius around the residue to make the calculations (in Angstroms)
set radius 13
#set radius for water
set radius2 [expr $radius + 5]

##################################################################################
#Enter the name for the output file
set filename1 "Water_Bridges_dmpc60_13A.csv"

#Set H-bond definition criteria
set cutoff 3.51
set angle 30.1

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

#Open files for writing
set fid1 [open $filename1 w]
set fid1Log [open $filename1.log w]

# Create file header
puts $fid1
"frame_write\tNlipids\tWaters\twater_donors\twater_acceptors\twater_hBonds\twater_1hBonds\twater_2hBonds\twater_3hBonds\twater_4hBonds\twater_m4hBonds\twater_avghBonds\tself_hBridges\tinter_hBridges\tinter_1hBridges\tinter_2hBridges\tinter_3hBridges\tinter_4hBridges\tinter_m4hBridges\tinter_avghBridges\tinter_dahBonds\tinter_ddhBonds\tinter_aahBonds"

#Wrapping the all molecules around the selected residue
pbc wrap -centersel "resid $resid" -center com -all

#####################################################################################
#Making a list of water and lipids molecules inside a sphere defined
around a residue
set water [atomselect top "same residue as (resname SOL) and within
$radius2 of (resid $resid and name CD)" frame $frame]
#selecting some particular atoms.....
set lipids [atomselect top "(resname DMP) and (name CD and within
$radius of (resid $resid and name CD))" frame $frame]

for {set frame 1} {$frame < $num_steps} {incr frame} {

        $water frame $frame
        $water update
        $lipids frame $frame
        $lipids update

         puts "Starting calculus on frame $frame"

        #write the number of residues found
        puts "water: [llength [lsort -integer -unique [$water get residue]]]"
        puts "water: [lsort -integer -unique [$water get residue]]"
        puts "lipids: [llength [lsort -integer -unique [$lipids get residue]]]"
        puts "lipids: [lsort -integer -unique [$lipids get residue]]"

        set Nwaters [llength [lsort -integer -unique [$water get residue]]]
        set Nlipids [llength [lsort -integer -unique [$lipids get residue]]]
        set LipidsMoleculesNumber [llength [lsort -integer -unique [$lipids
get residue]]]

         #Count H-bonds in selection
         set lipid_water_hBonds [measure hBonds $cutoff $angle $lipids $water]
         set water_lipid_hBonds [measure hBonds $cutoff $angle $water $lipids]

         $water delete
         $lipids delete

        #writing the number of lipids_water_hBonds found
         set n 0
         foreach a [lindex $lipids_water_hBonds 0] {
                         set n [expr $n + 1]
         }
         puts "lipids_water_hBonds found:# $n #"

         #writing the number of water_lipids_hBonds found
         set n 0
         foreach a [lindex $water_lipids_hBonds 0] {
                         set n [expr $n + 1]
         }
         puts "water_lipids_hBonds found:# $n #"
         ....................................
         .................................... 

-- 
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