SDA
Simulation of Diffusional Association
(version 6)
Changes in 6.00 (January 2010) and 6.02 (September 2010)
- Added functionality for docking proteins on metal (gold) surfaces and computing
the associated pmf. See also three new examples.
- A trajectory analysis tool was included in the SDA packaged. This can be found in auxi/traj_analysis
- Added functionality for rigid-body docking of two macromolecules with 1 example
for protein-protein docking.
- Added example for protein-protein electron transfer rate calculations.
- Added examples for the use of apbs instead of uhbd for electrostatic potential
calculations.
- New parameter input format. For easier extension, the parameter
input format has been changed. A conversion program
(convert_sda5_to_sda6_input) reads the old format and writes out
the new format.
- The format of how the reaction center is defined has changed. Now
the atoms of the reaction center of both proteins are in one file.
Also for this, a conversion program is included (rxna2rxnaC). This
is called automatically from the parameter conversion program.
Changes in 5.01
- Added an extra force (nonpolar/hydrophobic desolvation force)
calculated by multiplying the accessibilities
of atoms of one solute with a special grid for the second
solute. This grid is called the hydrophobic desolvation grid and this term can
approximate the interaction due to buried solvent accessible
area. The program to calculate suitable grids is mk_hd_grd.
- Option to calculate electron transfer rate constants has been
added. These
calculations are done when icommrxn=4. Reaction atom pairs should
have
pre-calculated coupling constants to respective donor or acceptor
sites - this can be done using the program HARLEM.
- The program to calculate electrostatic desolvation grids has
been changed to take into account the lack of ions in the solvent layer
between close solutes (separated by less than the ion diameter).
- The program sda-ener has been added. It recalculates
energies of previously recorded encounter
complexes with any user-supplied parameters. >
- The program sda-koff has been added. It monitors how
predefined
contact pairs are lost during Brownian dynamics of proteins starting
from a bound complex.
- The maximal dimensions of the grids have been uncoupled. It is
possible to
define different maximal dimensions for different types of grids as
well
as
for different proteins. The grid spacing is not fixed to 1
Å
anymore.
- The random number generator has been replaced with a better one
(randgen of R.Chandler and P.Northrop).
- The ECM effective charges used in SDA have been
changed. Variant _R of effective charges are used in SDA5, while
charges used as input to SDA4.23 are
the variant _E, see details here.
- The input file format has been changed, i.e. some input
parameters have been reordered. The output file format has been changed
slightly.
- A trajectory analysis tool was included in the SDA packaged. This can be found in auxi/traj_analysis.
$LastChangedDate: 2010-10-06 15:40:58 +0200 (Wed, 06 Oct 2010) $ by $Author: richtesn $
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