AMBER Archive (2009)

Subject: Re: [AMBER] LJ parameters for HO and HW

From: Jason Swails (jason.swails_at_gmail.com)
Date: Sat Nov 07 2009 - 23:50:03 CST

Hello,

The reason for HO atoms (hydrogens bonded to oxygens) have no van der Waals
radius (A and B L-J coefficients) was covered in the mailing list recently
here http://archive.ambermd.org/200910/0304.html. Atomic charges in amber
are put as point charges at the nuclear locations of each atom. Nuclear
locations exist regardless of whether or not an atom has a vdw sphere, so
these hydrogens must certainly have a charge (no hydrogen bonded to an
oxygen will have 0 charge), but no vdw radius.

Also note that van der Waals potential terms and electrostatic potential
terms are fundamentally different. Electrostatic interactions are simple
coulombic interactions arising from fixed charges. VDW interactions are
more subtle, and are actually an empirical fit (using r^-12 and r^-6 terms)
to model dispersion effects of electron "clouds" (more accurately the
respective orbitals of neighboring systems). Dispersion is a quantum
mechanical effect that arises from the correlated motions of electrons which
is why L-J is needed at all (since simple electrostatic potentials cannot
capture this effect).

Hope this helps. Good luck!
Jason

On Sun, Nov 8, 2009 at 12:21 AM, manoj singh <mks.amber_at_gmail.com> wrote:

> Hi all !
>
> I am having trouble in understanding why the L-J parameters for HO and HW
> is
> 0.00, as written in parameter file.
>
> If it is 0, then how amber manages to treat charges on it.
>
> --
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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