SDA
Simulation of Diffusional Association
(version 6)

Output

'complexes' - complexes satisfying ncec-contact (default: 2 contact) reaction conditions defined by iwrec and nwrec,.  These complexes can be processed further to check interaction energies calculated by SDA (structure of file 'complexes').

'trajectories' - A complete trajectory whose number is given by nrec or all trajectories if nrec is negative  These complexes can be processed further to make a movie of a Brownian dynamics trajectory, to visualize encounter complexes or check interaction energies calculated by SDA, using auxiliary programs from the SDA distribution.

• Parameters of simulations as read in from input file(s).

• Each nprint runs, the number of runs done and the ratio of reaction events at every reaction distance are printed. This allows the main results (association rate constants) to be retrieved in the case that the program is interrupted before it finishes.

• Mean residence times are computed and printed (after the simulations are finished) in every 1 Å slab of inter-solute center-to-center separation.

• In the case of protein-surface docking only(ibox>0), mean residence times are computed and printed (after the simulations are finished) in every cell (dx;dy;z=0-b); the surface is divided by 12x12 cells.

• In the case of protein-surface docking only(ibox>0), the average energy and number of visiting events in each 0.5 Å thick slab of inter-solute center-to-center vertical separation.

• The main results of simulations - generally the association rate constants - are printed for every distance window and every number of contact pairs.

• The execution time of the program is printed for initialization and simulation parts.

• At the end of the simulations, the statistics over all runs are computed and printed out. These are:

  • number of Brownian dynamics steps during all simulations;

  • the duration of simulations in ps;

  • above value scaled per run;

  • number of solute overlaps (when the step is repeated) that occurred;

  • number of boosts, when the solutes were artificially displaced.

fort.44 - calculated solvent accessibilities for each accessible atom of solutes 1 and 2

fort.66 - a table giving the length (number of BD steps) of each trajectory. 

fort.77 - this file contains the values of the electrostatic and desolvation potentials of solute 1 and solute 2 along 5 selected lines in 3-dimensional space; a section through the exclusion grid in ascii format in the plane passing through the center of the solute 1; reaction atom information.  This file is designed to assist in checking if the input files are correct and/or read as expected.

fort.99 - this file gives the occurrence of reaction atom contacts.  The first half of this file gives the number of contacts observed at each specified contact distance for each pair of reaction atoms.  In the second half, the number of contacts is counted differently - only the first occurrence of the contact in a Brownian dynamics run/trajectory is counted.

The file with the name specified in BLOCK 13 of the input file has intermediate results written every nprint runs.  It can be used to check the status of a long SDA run, or to compute association rate constants from incomplete runs of SDA.  It has a table of fractions of reactive trajectories among the trajectories so far simulated.

pmf.dat – calculated only for protein adsorption on a solid state surface (ibox=1) and if input parameter parameter fee_en >0. The file contains the potential of mean force (pmf) and minimum binding energy as a function of the distance between a protein geometric center and surface atoms of the solid state cluster; and additionally, the adsorption free energy (dG). All energy values are given in units of kT.

tmp-pmf.dat – calculated only for protein adsorption on a solid state surface (ibox=1) and if input parameter parameter fee_en >0. Temporary file for checking the status of free energy calculations. Contains protein-surface distance as well as pmf and minimum energies at the current calculation step (distance from the surface).

pmf-conf.dat – calculated only for protein adsorption on a solid state surface (ibox=1) and if input parameter parameter fee_en >0. The file can be used for generation of pdb structures corresponding to the minimum binding energy at each protein-surface distance (here, distances between centers of a protein and solid state cluster). The first 11 columns in the file are the same as in 'complexes' (the 12^th column contains the minimal total binding energy at the corresponding z value, see also structure of file 'complexes'). The columns 13 and 14 are total electrostatic and Lennard-Jones energies at the corresponding protein position.

[Back to Index]

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