[Apbs-users] Re: convert uhbd input to apbs

[Fabrice L. <Fab...@ma...>]

Hi,
I'm doing some comparison between UHBD and APBS on a series of test 
calculation. I have a similar setup for both programs on a bimolecular 
complex (grid spacing, solute and solvent dielectric, ionic strength, 
temperature, etc) . I have calculated the coulombic energy of 
interaction between the 2 molecules of the complex using UHBD and APBS. 
The calculations performed as described below (message from december 
19) give similar results between UHBD and APBS.
I'm interested now in the total electrostatic energy term for the 
complex ("print elec energy  all end" in UHBD). I don't get equivalent 
results between the 2 programs. Is this just due to the difference in 
grid mapping between the 2 programs ? Is there any correspondence 
between the numerical values given by the 2 programs as the total 
electrostatic energy ?

If I want to calculate the the electrostatic energy to transfer the 
complex from the gas phase (dielectric = 1) to the aqueous phase 
(dielectric 78), it can be done with UHBD in a single calculation 
("print elec tenerg all end") after printing and subtracting the self 
energy ("print elec self   all end") and the coulombic grid 
contribution ("print elec fdcoul all end"). What is the correct way to 
do this calculation with APBS ?


On Friday, December 19, 2003, at 01:14 PM, Nathan A. Baker wrote:

> Hi Fabrice --
>
> I get this question fairly frequently so I'm going to Cc my reply to
> the APBS mailing list.
>
> There are two ways to get the Coulombic energy of a complex:
> 1.  Use Coulomb's law (apbs/tools/manip/coulomb) and scale by the
>     appropriate dielectric coefficient.
> 2.  Solve Poission's equation with a homogeneous dielectric
>     coefficient to determine the energies of protein A, protein B, and 
> the
>     A-B complex.  The proteins' atoms must stay at exactly the same
>     place on the grid for each calculation; likewise, the grid
>     spacing, position, etc. cannot change between calculations.  The
>     Coulombic energy change for forming the complex is then:
>     E(AB) - E(A) - E(B)