VMD-L Mailing List

From: Florentina Tofoleanu (florentina.tofoleanu_at_gmail.com)
Date: Thu Nov 26 2009 - 05:16:34 CST

Hello VMD users,

I apologize if this has been discussed here before, but I haven't found any
reference to it in the Mailing list.

I have a small issue regarding the variant number of hydrogen bonds in the
following situations:

a) Hydrogen Bonds Representation
b) using the Hydrogen Bonds counting/plotting in VMD 1.8.7
c) counting the HBs with the following script:

set mol1 [mol new XXX.pdb type pdb waitfor all]
set sel1 [atomselect $mol1 all]

set mol [mol new XXX.psf type psf waitfor all]
mol addfile XXX.dcd type dcd waitfor all molid $mol

set sel2 [atomselect $mol all]
#$sel2 set mass [$sel1 get mass]

# cleanup
$sel1 delete
$sel2 delete
mol delete $mol1

set outfile [open file.dat w];

set numframes [molinfo $mol get numframes]

set refA1 [atomselect $mol "protein and segname X1"]
set refB1 [atomselect $mol "protein and segname X2"]

for {set frame 0} {$frame < $numframes} {incr frame} {

$refA1 frame $frame
$refB1 frame $frame

$refA1 update
$refB1 update

set nhb [llength [lindex [measure hbonds 3.0 30 $refA1 $refB1] 0]]

puts $outfile "$frame $nhb"

}

close $outfile

In each case there are shown different values for the same timeframes and
the same cutoffs 3A distance and 30degrees angle. The lowest values
registered are in case c), followed by case b). Both have some zero values
for the no. of HBs, which doesn't happen in the HBs Representation.

Which is the more realistic one?

And if case c), could anyone give the script for showing the bonds in the
representation?

Thank you,

Florentina 

-- 
Florentina Tofoleanu
Postgraduate Research Fellow
Theoretical and Computational Biophysics Group
University College Dublin
School of Physics, Rm. 110
Belfield, Dublin 4, Ireland