From: soroush ziaei (
Date: Sun Dec 23 2018 - 09:51:17 CST

is it correct to load PDB format of molecules?
actually, I have loaded the system completely and then separated this into two structure with all of the frames in order to specify donor and acceptor but an error appears:

atomselect: cannot parse selection text: 2.pdb
atomselect: cannot parse selection text: 2.pdb
    while executing
"atomselect $currentMol $atomselectText1"
    invoked from within
"if [info exists arg(sel1)] {
     set molid [$arg(sel1) molid]
     if { $polar } {
        set sel1 [atomselect $molid "([$arg(sel1) text]) and (name..."
    (procedure "::hbonds::hbonds" line 127)
    invoked from within
"::hbonds::hbonds -gui 1 -dist $::hbonds::guiDist -ang $::hbonds::guiAng -writefile $::hbonds::guiWrite -outdir $::hbonds::guiOutdir -frames $::hbonds:..."
    invoked from within
".hbonds.control.button invoke"
    ("uplevel" body line 1)
    invoked from within
"uplevel #0 [list $w invoke]"
    (procedure "tk::ButtonUp" line 24)
    invoked from within
"tk::ButtonUp .hbonds.control.button"
    (command bound to event)

what does this mean?!

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From: Vermaas, Joshua
Sent: Sunday, December 23, 2018 5:10 PM
Subject: RE: vmd-l: h-bond

"Molecule" = VMD molecule, not molecule like how a chemist would think of them. Basically though you make a representation like any other, but instead of choosing a VDW or licorice representation, you choose h-bonds. If both the donor and acceptor are in the atom selection used to draw the representation, you'll see little dashed lines indicating where the hydrogen bond is.

On 2018-12-22 17:05:52-07:00 wrote:
Hi vmd users,
How to visualize hydrogen bonds between water box and a drug molecule in it using VMD?
Could someone let me know the steps?
by the way,  i have read the VMD User’s Guide and i saw somewhere in this paper that written: The two selections must be from the same molecule!!  how?!
Please help.
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