AMBER Archive (2009)

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

From: Cihan Aydin (cihan.aydin_at_umassmed.edu)
Date: Mon Jul 06 2009 - 10:13:39 CDT

I actually have a question here,

How are the van der Waals interactions treated in united-atom force
fields? Still with the Lennard Jones 6-12 potential? Or is there a
special parametrization for molecules?

Thanks,

Cihan

On Sat, 2009-07-04 at 07:01 +0200, FyD wrote:
> 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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> 

-- 
Cihan Aydin
UMass Graduate School of Biomedical Sciences
PhD Student @ Schiffer Lab

364 Plantation St. LRB 970M
Worcester, MA 01605

cihan.aydin_at_umassmed.edu
+1 (508) 856-3430

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