Re: [AMBER] please, units of LENNARD_JONES_ACOEF in prmptop?

From: Paul S. Nerenberg <psn.berkeley.edu>
Date: Tue, 13 Jul 2010 17:31:13 -0700

Hi Jose,

I believe that those units are correct (see http://ambermd.org/Questions/vdwequation.pdf)
. Keep in mind though that the interatomic distances between the
*closest* atoms involved in the salt bridge are likely about 2 (and
that 2^12 is already 4096). So ACOEF (which might be on the order of
10^5) will be divided by something of the order 10^3 (or more), and
BCOEF (which might be on the order of 10^3) will be divided by
something of the order 10^2 (or more). Thus both the repulsive and
attractive terms could end up being on the order of 10 kcal/mol, which
could then easily yield the results that you are observing (vdW
energies that are relatively close to zero). Your results seem pretty
reasonable to me, based on simulations my previous group did on salt
bridges...

Best,

Paul


On Jul 13, 2010, at 4:45 PM, Jose Borreguero wrote:

> Dear amber users,
>
> Are the units of LENNARD_JONES_ACOEF in prmptop (Kcal/mol * A^12)
> and the
> units of LENNARD_JONES_BCOEF (Kcal/mol * A^6) ?
>
> I wonder because the typical Lys - Gly salt bridge has
> electrostatics ~
> 70Kcal/mol, while only VdW ~ 2 Kcal/mol. The disparity of the energies
> surprised me.
> Similarly, the range of electrostatic energies between pair of
> residues has
> a much bigger variation than the range of VdW energies. For
> rubredoxin in
> the native state, the elec-range=[-99,80]Kcal/mol and the
> VdW-range=[-6,2]Kcal/mol. Is this expected?
>
> -Jose Borreguero
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber


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Received on Tue Jul 13 2010 - 18:00:02 PDT
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