SDA
Simulation of Diffusional Association
(version 6)

Installation

To install SDA, gunzip and untar the distribution package.  In the directory of the distribution package (referred to as $SDA_DISTRIBUTION_DIR) there are the following directories:

subdirectory of
SDA_DISTRIBUTION_DIR

 description
auxi/
 Auxiliary programs for sda
bin/
 Directory containing executables
doc/
 Documentation
ecm/
 ECM distribution
examples/
 Examples of SDA runs
src/
 Source files

SDA executables are in the bin/ directory.  If you need to recompile SDA, go to the src/ directory, edit the file called definitions to set your favorite fortran compiler. Then type
make
This will compile the main sda executable using your compiler and place it in the bin/ directory. 
You might need to modify the file maxdim.inc so that the executable will handle potential and atom coordinate file arrays of the size necessary for your needs. >
To make SDA calculate solvent accessible areas faster (details here), you need to obtain NACCESS and place its subroutines solva() and sortag()  in the src/ directory instead of the existing file solva.f and recompile SDA.

The other SDA executables (sda3g, sda-koff, sda-ener, sda-site) are compiled and executed in the same way as the main SDA executable.

The auxiliary programs can be compiled by changing directory to auxi/ and typing
make all
You might need to edit and recompile programs in this directory in order to adjust file arrays to the size necessary for your needs.
See files src/Makefile and auxi/Makefile for the compilation details .

Getting started

The SDA program itself is executed by typing in
$SDA_DISTRIBUTION_DIR/bin/sda_ifort < input-file > output-file

A description of the input file format is here , the output files are described here .

To run SDA, you have to prepare:

  • 2 pdb files of solutes and 2 pdb files with reaction atoms, 1 for each of the 2 solutes.
If electrostatic interactions are to be taken into account, then
  • 2 grid files with the electrostatic potential in UHBD format are needed, as well as 2 files containing effective charges calculated with ECM. 
If the forces due to desolvation are to be taken into account,
If the Lennard-Jones forces are to be taken into account
  • Lennard-Jones grid(s) of one solute (currently only solute no. 2) and the probe site identifier for each atom of the other solute (last column in pdb file) are needed.  See the description of the input file for details.
If protein adsorption on a solid state surface is to be simulated
  • the solid state surface should be represented as a slab of several atomic layers in PDB format. An Example for Au(111) is given at: aubs example. 
  • The solid surface can be modeled as a zero-potential surface or as a set of charged atoms. In the latter case, an electrostatic grid for the surface and a file that defines surface charges are needed.  See the description of the input file for details.

    • These pdb and grid files can be located anywhere as long as the relative or absolute paths to these files are given correctly in the input file.  Output files will be written in the directory where SDA is executed.  The main calculation results are written to standard output which can be redirected to a file as in the above execution example.


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     $LastChangedDate: 2010-10-06 15:40:58 +0200 (Wed, 06 Oct 2010) $ by $Author: richtesn $ Privacy Imprint