Changes in the sda 7.3.5 release: Feb. 2024 - Better documentation of the complexes file - Fixing problem that disallowed the compilerflag for debugging - Fix a problem in sdamm with calculations where oneway_surf_charge is set and debye hueckel approx is used - Corrected the exponent from 2 to 3 in the expression for the calculation of the translational diffusion coefficient of a solute moving near to and parallel to a surface. (make_bd_move_2prot.f90 line 194 and make_bd_move_sdamm.f90 line 145) - Fix a problem in sdamm forces with pprot1 always being pointed as a movable solute when a surface is present - Fixing a problem with out of bounds in ECM for large surface grids (tools/ECM/ecm_mainsubroutine.f90 line 777) - Fixing a problem with integer overflow in ECM for large surface grids, overflow occured at tools/ECM/ecm_mainsubroutine.f90 allocation of variable stor (line 339) , solved by using integer kind 8 on several places. - Added conversion script from SDA to BrownDye2 Changes in the sda 7.3.4 release: Feb. 2022 - Fixing problem related to compilation with gcc 11 by setting g++ standard to g++03. - Changed the default solution density in the HFBI-graphite example as the current value was too dense to converge. Changes in the sda 7.3.3d release: Jan. 2022 - Fixing problem related to diffent initialization syntax in gcc 10.3 Changes in the sda 7.3.3 release: Oct. 2021 - Fixing problem with read_record to set center always to 0 Changes in the sda 7.3.2 release: Sept. 2021 - Fixing different docking results for parallel and serial processing - Documentation updates Changes in the sda 7.3.1 release: March 2021 - Added example setting up a simulation box and analyzing Brownian dynamics simulations which mimic fluorescence recovery after photobleaching (FRAP) experiments. The tutorial will follow the procedure and use parameters described in the paper "Line-FRAP, a versatile method to measure diffusion rates in vitro and in vivo" (D. Dey et al, J. Biol. Chem, in press), but with much simplification. Changes in the sda 7.3 release: November 2020 - Added new functionality for long-range Debye-Hückel and hydrodynamic treatments of solute-surface interactions - Added analysis tool for monitoring solute adsorption on a surface - New model for hydrodynamic interactions in the presence of surfaces. - New Debye-Hueckel models for image charge electrostatics and electrostatics in the presence of charged surfaces. - For a description of the HI and DH models - see Reinhardt et al. XXX - New tool for calculating translational and rotational diffusion coefficients from simulations. This tool replaces the two separate previous tools. It is considerably faster than the old tools, uses less memory, and does not require separate trajectory files to be concatenated into one large file. For simulations that include surface is can calculate the coefficients in height-dependent bins above the surface and decompose them into components due to diffusion parallel and perpendicular to the surface. Changes in the sda 7.2.4 release: March 2020 - Converted python 2.7 scripts to version 3.6 - TestAddHydrogens.py and TestReadPDB_SDA.py removed. Those were only for testing. - MergeAddAtoms.py, GetAddAtomJson.py, script_AddAtomJson.py and PDB2PQR_sda.py is not updated to python 3 as the python module Propka is not available for python 3.6 or later. Changes in the sda 7.2.3 release: April 2019 - Fixed bug in auxiliary tool "Bootstrap_multiCPU.py" for bootstrap calculations for association rate constants by replacing "==" with "is" as "==" no longer worked correctly if the element for comparison was a numpy array object. - Converted python scripts to run on python 2.7 and 3.7. - Documentation of examples brought up to date - Documentation of input, output and FAQ corrected and improved and some documentation restructured - Scripts and documentation for preparation of small molecules revised, including updated charge assignment procedure. - Distribution for this version onwards with EUPL Changes in the sda 7.2.2 release: July 2017 - Fixed bug that means that the positions of effective charges and solvent accessible atoms were not set correctly at the start of a simulation containing flexible solutes. This bug only affected the start of simulations, and the positions would be correct after the first transition in conformation. If potential conformational transitions were accepted using either the minimum energy or Metropolis criteria, it is possible simulations may have been trapped in very low energy configurations due to very favourable overlapping charge interactions. - Option vert_excl added so that decision on whether to check for excluded volume violations depends on the height (z coordinate) of the mobile solute, rather than the centre-to-centre distance between solutes. This behaviour is automatically turned on when the solute is defined as a surface. - Variable timestep can now depend on height above a planar solute to improve performance. - Option (half_sphere) to make starting position lie on a spherical cap rather than a sphere added - New options (xcent, ycent, zcent) to define the centre of simulation geometry relative to fixed solute added. - Changes made to genbox tool. Previously a user could set a fixed concentration and number of molecules in the input file, and the tool would calculate the required cubic volume. As an alternative, the box size and concentration can now be set, and the number of molecules calculated. Also, sorting the solutes by size before packing into the box can now be turned off. In some cases it could result in all smaller solutes being placed near the box boundaries, rather than dispersed in the box. - Changes made to the rdf tool so the distribution of all solute types around a single type can be calculated. - New tool (centrosymmetry_potential.py) which compares the values of potential grids at regular distance intervals along the principal axes in each direction. Changes in the sda 7.2.1 release: Oct 2016 - Fixed a bug that mean that, by default, excluded volume checks were not performed in two solute simulations Changes in the sda 7.2 release: July 2016 - Introduction of a new datastructure named dynamic tubular grid (DT-Grid) for sparse interaction grids with efficient compression and fast random data access. - New grid conversion tools: 'UHBD2dtgrid' for converting UHBD format grid files into DT-Grid format files, and 'dtgrid2UHBD' for converting DT-Grid format grid files into UHBD format grid files. - A new example to show how to use the DT-Grid data structure under examples/au3his. - Bugfix to Debye-Hueckel correction. Previously solute were treated as Debye-Hueckel spheres with charges equal to the sum of their effective charges. This has now been changed so that the formal charge on the solute can be defined in the SDA input file. - Small bugfix to increase the character array that holds the name of restart files. - New option to calculate the analytical correction in the Northrup, Allison and McCammon method to account for non-zero but centrosymmetric interactions at the b surface. - New option to ignore the excluded volume check during two solute simulations. Allows soft-core repulsion interaction to be used instead. - Python scipts for setting up solute grids modified for consistency with current version of webSDA. - New tool (rdf) to calculate radial distribution functions from many molecule simulations, see tool documentation. - New tool (convert_traj_SDAMM) to convert SDA 7 trajectrories to older SDAMM format. Replaces places previous option in read_record to convert. - New tool (calc_solvaccess) for calculating solvent accessibility of atoms in a PDB file. - Updated electron transfer example to use the Pathways plugin to VMD in place of HARLEM. - Parallel version of mk_LJ_grd - Documentation in the Makefile and HTML for compilation on MacOS - Genbox updated to allow a fixed number of molecules of a certain type to be added - New input parameter mem_traj_frames defines how many trajectory frames to hold in memory before writing to disk, replaces previous parameter max_array_traj, which could prevent writing of a restart file if not set to a multiple of the total number of solutes. - New input parameter stop_traj stops association calculation trajectories when the most strict reaction criteria definition is met. - Updated documentation of SDA website FAQ describing how to set up simulations. Changes in the sda7.12 release: July 2015: - Corrected a bug that could lead to the wrong atomic radii being used to generate exclusion grid. Changes in the sda7.11 release: June 2015: - The potential of mean force calculation has been updated: - To improve the modularity of the code. - To make minor changes to the sampling of configurations near to the surface. - To ensure correct sampling of solute rotations. - The example in the au3his directory has been changed. - The radius used to define the local volume for the mean-field hydrodynamic approximation is now defined by user input (lvol_rcut -see documentation). - New tools to define reaction criteria for small molecule-protein interactions, and to allocate test charges to small molecules have been added in the auxi directory. Changes in the sda7.1 release: March 2015: - Debye-Huckel approximation to long-range electrostatic interactions. - Calculation of potential of mean force for interactions of solutes with planar surfaces. - Documentation updates. - Improvement to calculation efficiency and scaling. - Removing possibility to include naccess since it is now possible to set the input parameter 'save_access'. This allows the reuse of solvent accessible surface calculations in later runs. - Addition of kmeans clustering tool. Changes in the sda7 release: November 2013: - SDA and SDAMM codes merged into one release. - Migration of source code from fortran 77 to fortran 90. - Bimolecular simulations can now be run in parallel with OpenMP. - Solute flexibility included by allowing transitions between rigid solute conformations. Changes in the sda6 release, preliminary: January 2010, complete: September 2010: - Added functionality for docking proteins on metal (gold) surfaces and computing the associated pmf. See also three new examples. - 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 the sda5 release, spring 2009: - 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 Ċ 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 SDA 4.23 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. - changed max grid dimension in auxi/mk_*_grd to 200 - switched to static option in src/Makefile, because dynamic executables are found not to work on some systems