From: Vermaas, Joshua (
Date: Sun Dec 23 2018 - 07:40:26 CST

"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 Userís 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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