README for protein-RNA APBS example

$Id: README.html 1336 2008-12-21 23:25:17Z sobolevnrm $

This is example is taken directly from

García-García C, Draper DE. Electrostatic interactions in a peptide-RNA complex. Journal of Molecular Biology. 331 (1), 75-88, 2003. http://dx.doi.org/10.1016/S0022-2836(03)00615-6
with the minimized PDB files kindly provided by David Draper. It uses the change in binding free energy with ionic strength to estimate the change in number of ions "bound" (diffusively) to RNA upon protein binding.

A more comprehensive walkthrough of this example is available online.

The APBS results agree reasonably well with Draper's calculations; there are some differences in parameterization, surface definitions, etc. that lead to small differents in the results.

To run this example, set the environmental variable APBS to your current APBS executable; e.g.,

export APBS=/path/to/apbs/executable
		
in bash or
setenv APBS /path/to/apbs/executable
		
in tcsh. Then simply type 'make' to run the example.

Input file Description APBS version APBS results Draper PB results Draper experimental results
      n = -(d Δ G)/(d ln [KCl])/RT -d( Δ G)/(d log10 [KCl]) (kcal) n = -(d Δ G)/(d ln [KCl])/RT -d( Δ G)/(d log10 [KCl]) (kcal) n = -(d Δ G)/(d ln [KCl])/RT -d( Δ G)/(d log10 [KCl]) (kcal)
'make all' Run a series of binding energy calculations at different ionic strengths APBS 1.0.0 -(4.52 ± 0.08) 6.2 ± 0.1 -(4.3 ± 0.2) 5.9 ± 0.2 -(4.4 ± 0.2) 6.0 ± 0.2
Please see the ChangeLog or the APBS documentation for more information.