Hi,

We are trying to calculate the interaction energy for a protein - protein complex and used apbs to calculate the PB energy. While analyzing our result, we were confused and had the following questions:

1. The input file that we use is the following:

read
    mol pqr protein.pqr
end
elec
    mg-auto
    dime 161 193 161
    cglen 102.8602 121.8832 96.3985
    fglen 80.5060 91.6960 76.7050
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 78.5400
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
    write pot dx pot
end
elec
    mg-auto
    dime 161 193 161
    cglen 102.8602 121.8832 96.3985
    fglen 80.5060 91.6960 76.7050
    cgcent mol 1
    fgcent mol 1
    mol 1
    lpbe
    bcfl sdh
    pdie 2.0000
    sdie 2.0000
    srfm smol
    chgm spl2
    sdens 10.00
    srad 1.40
    swin 0.30
    temp 298.15
    calcenergy total
    calcforce no
end
print elecEnergy 2 - 1 end
quit

The resulting apbs energy is a positive value. Is this because the way the input file works is Ehomogenious -Einhomogenious? If so, do we need to multiply the resulting value by -1?

2. In our MD simulations, we used a dielectric constant of 1. However, the dielectric constant used in the above input file is 2. Should we change pdie to 1? If so, will we need to change sdie to 1 to get the homogenous part of the apbs energy?

Thank you very much
Pinar.



2008/11/21 Gernot Kieseritzky <gernotf@chemie.fu-berlin.de>
Hi!

> these molecules need to be *perfectly* aligned since you're relying on
> this alignment to cancel self-interaction energies.  Please be sure to
> check that the atoms are in the same locations after alignment.

Yes, I forgot the self-energy. Perfect alignment by rigid-body alignment
is not possible in her case since the subunits will adopt slightly
different conformations in the monomer case compared to the dimer
situation.

So, Pinar, what you should do to compute the association energy for the
protein complex (I guess, this is what you ultimately want to achieve)
is to compute the total electrostatic energy for the dimer ( E(d) ) and
the monomers ( E(m1), E(m2) ) individually and then compute the
difference

E(d) - ( E(m1) + E(m2) )

How to compute the total dielectric energy?

E(x) = (coulomb energy of x) + E(x, inhomogenious) - E(x,  homogenious)
      ^^^^^^^^^^^^^^^^^^^^^   ^^^^^^^^^^^^^^^^^^^^  ^^^^^^^^^^^^^^^^^^
      use 'coulomb.c' in the  APBS with pdie!=sdie  APBS with pdie=sdie
      APBS distribution with                        and no ions
      eps = pdie

The difference E(x, inh) - E(x,hom) will ensure that the grid artifact
cancels.

To compare with possible experimental values in case of protein-protein
association you will also need to include the non-electrostatic
contribution to the solvation energy and add this to E(x).

Greetings,
Gernot


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--
pinar