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

From: Jose Borreguero <borreguero.gmail.com>
Date: Wed, 14 Jul 2010 10:56:08 -0400

My goal was to compare energies between pair of residues for two proteins
with the same topology but different sequence. Unfortunately, the
electrostatic energy shows such huge variations than this comparison seems
meaningless to me.

For purposes of detail:

In the salt bridge I looked, this were the distances and energies:
NZ q=-0.385 CD q= 0.805 dist=3.15 ele=-32.76 vdw= 0.26
NZ q=-0.385 OE1 q=-0.819 dist=2.77 ele= 37.88 vdw= 1.51
NZ q=-0.385 OE2 q=-0.819 dist=3.31 ele= 31.67 vdw=-0.16
HZ1 q= 0.340 CD q= 0.805 dist=3.94 ele= 23.08 vdw=-0.00
HZ1 q= 0.340 OE1 q=-0.819 dist=3.34 ele=-27.68 vdw=-0.01
HZ1 q= 0.340 OE2 q=-0.819 dist=4.05 ele=-22.84 vdw=-0.00
HZ2 q= 0.340 CD q= 0.805 dist=3.05 ele= 29.82 vdw=-0.02
HZ2 q= 0.340 OE1 q=-0.819 dist=3.04 ele=-30.42 vdw=-0.02
HZ2 q= 0.340 OE2 q=-0.819 dist=2.86 ele=-32.38 vdw=-0.02
HZ3 q= 0.340 CD q= 0.805 dist=2.31 ele= 39.37 vdw=-0.02
HZ3 q= 0.340 OE1 q=-0.819 dist=1.76 ele=-52.47 vdw= 0.63
HZ3 q= 0.340 OE2 q=-0.819 dist=2.69 ele=-34.34 vdw=-0.03

Adding this energies, the salt bridge ends up with:
ele=-71.0725 vdw=2.1070

-Jose

On Tue, Jul 13, 2010 at 8:31 PM, Paul S. Nerenberg <psn.berkeley.edu> wrote:

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 14 2010 - 08:30:04 PDT
Custom Search