Re: [apbs-users] Binding energy calcuation via two thermodynamic cycles...

[Baker, N. <Nat...@pn...>]

Hello –

Differences like these are almost always due to lack of convergence of the results with respect to grid spacing.  Given the size of the systems and the relatively high charge density of actin, I’m guessing that’s the issue here as well.

Thanks,

__________________________________________________
Nathan Baker
Pacific Northwest National Laboratory
Tel:  +1-509-375-3997
http://nabaker.me<http://nabaker.me/>

From: tj [mailto:jai...@gm...]
Sent: Wednesday, June 13, 2012 11:44 AM
To: apb...@go...
Subject: [apbs-users] Binding energy calcuation via two thermodynamic cycles...

Hi,

I have a question on calculating the total electrostatic binding energy using APBS, but via two thermodynamic routes:

Route1 : Calculate the solvation contribution(as in print statements for the FKBP/1d7i-dss example) + coulomb calculation(using the coulomb program). e.g.
# CHANGE IN SOLVATION ENERGY UPON BINDING
print elecEnergy complex-solv-fine - complex-ref-fine - dss-solv-fine + dss-ref-fine - 1d7i-solv-fine + 1d7i-ref-fine end


Route2 : Calculate difference of charging energies as in print statements for examples actin-dimer. e.g.
# COMBINE TO GIVE BINDING ENERGY
print elecEnergy complex - mol2 - mol1 end

In the case of the FKBP/1d7i-dss example, the two methods return approximately the same value. Details of the output produced are below:
For the example 1d7i-1dss
================
Command
-----------
apbs apbs-mol.in

Thermodynamic Cycle based on Solvation/Desolvation Energies:
------------------------------------------------------------
Coulomb complex : -1.330929222200e+05 / 2(pdie)  - Using the coulomb program
Coulomb dss-min : -4.251892874134e+02 / 2(pdie)
Coulomb 1d7i-min: -1.326437989481e+05 / 2(pdie)

Binding Coulomb Energy: -11.97036 (Coulomb complex - Coulomb dss-min - Coulomb 1d7i-min)
Binding Solvation Energy : 14.42500 (complex-solv-fine - complex-ref-fine - dss-solv-fine + dss-ref-fine - 1d7i-solv-fine + 1d7i-ref-fine)

Binding Electrostatic Energy1 : 2.45464 (Binding Solvation Energy + Binding Coulomb Energy)

Thermodynamic Cycle based on Charging/Discharging Energies:
-----------------------------------------------------------------------
Binding Electrostatic Energy2 : 2.19264 => (complex-solv-fine - dss-solv-fine - 1d7i-solv-fine)

Comparison:
-----------
Binding Electrostatic Energy1 ~ Binding Electrostatic Energy2


However, for the actin-dimer example, the values are not close at all:
For the example actin-dimer
==================

Command
-----------
apbs apbs-mol-auto.in

Thermodynamic Cycle based on Solvation/Desolvatin Energies:
-----------------------------------------------------------------------
Coulomb complex : -8.212523932986e+05 / 2(pdie)  - Using the coulomb program
Coulomb mol2 : -4.121924924143e+05 / 2(pdie)
Coulomb mol1: -4.122022764715e+05 / 2(pdie)

Binding Coulomb Energy: 15.71188E+02 (Coulomb complex - Coulomb dss-min - Coulomb 1d7i-min)
Binding Solvation Energy : 1.054579051270E+02 => (complex - complex-ref - mol1 + mol1-ref - mol2 + mol2-ref)

Binding Electrostatic Energy1 : 16.7665E+02 (Binding Solvation Energy + Binding Coulomb Energy)

Thermodynamic Cycle based on Charging/Discharging Energies:
------------------------------------------------------------------------
Binding Electrostatic Energy2 : 1.048683060915E+02 => (complex - mol1 - mol2)

Comparison:
--------------
Binding Electrostatic Energy1 != Binding Electrostatic Energy2

In the second case the agreement is not good while in the first case it is quite good. I realize that the first route is what is usually recommended because of the grid cancellations of the self-energies. However, I have seen the binding electrostatic energy calculation done using the the second route in several examples. From my understanding of the apbs-smol-auto.in(actin-dimer exmaple), the grid is centered on the complex for all the three calculations, so I am not sure, if the difference arises because of grid artefacts.

Thanks for your help.