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 and type
make sdaG77
This will compile the main sda executable using the GNU fortran compiler and place it in the bin/ directory.  Alternative compilers can be used with these commands:
make sdaPGF
make sdaIFC
These use the Portland and Intel fortran compilers, respectively, see src/Makefile.
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. >
The SDA program itself is executed by typing in
$SDA_DISTRIBUTION_DIR/bin/sdaG77 < 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 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,

• the electrostatic and the hydrophobic desolvation grids of each solute 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 that can be redirected to a file as in the above execution example.

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 .

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