AMBER Archive (2009)

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

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Sat Jul 04 2009 - 00:01:58 CDT

Dear Taufik Al-Sarraj,

You might find these 2 web sites interesting:
http://en.wikipedia.org/wiki/Van_der_Waals_bonding
http://en.wikipedia.org/wiki/Hydrogen_bond

http://en.wikipedia.org/wiki/Electrostatics ?

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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