AMBER Archive (2009)

Subject: Re: [AMBER] H-bond vs. VdW

From: FyD (
Date: Sat Jul 04 2009 - 00:01:58 CDT

Dear Taufik Al-Sarraj,

You might find these 2 web sites interesting: ?

regards, Francois

> Hello,
> 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,
> Taufik
> 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
> correctly.

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