AMBER Archive (2009)

Subject: [AMBER] H-bond vs. VdW

From: Taufik Al-Sarraj (
Date: Fri Jul 03 2009 - 13:48:12 CDT


This is a background question.

There are many molecular modeling studies that examine Hydrogen bonding
formation and evolution over a specific time scale, are there studies
that look at VdW interaction between two atoms (or group of atoms) over
a specific time scale in AMBER?

i want to make this argument : Hydrogen bonds are more readily studied
by molecular modeling in comparison with van der Waals interactions. but
i don't have the support.

Or should i make the argument that hydrogen bonds can be isolated and
studied separately while VdW interactions cannot be isolated and
therefore cannot be studied independently?

Thank you for your help,

P.S. the system i am studying consists of a zipper protein and a DNA
strand, hydrogen bonds can tell us where the DNA backbone and zipper
interact. VdW can tell us a little about affinity if i can monitor it

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