SDA
Simulation of Diffusional Association
(version 6)


Input file: SDA5 and SDA6 formats



New format (used in SDA v6):

The input file consists of a series of blocks of input parameters. The format of each block of the input file is as follows:
name-of-parameter parameter-value
Here is an example file:

# BLOCK (01)
  dseed 256.d0

# BLOCK (02)
  nrun 1000
  nprint 1
  nrec 0
  timemax 2.e4

# BLOCK (03)
  p1f p1.pdb
  p2f p2.pdb

# BLOCK (04)
  probep 0.5
  probew 1.4
  hexcl 0.5
  thres 0.0

# BLOCK (05)
  dm 0.0123
  dr 1.36e-4
  dr1 1.36e-4
  irot2f 0

# BLOCK (06)
  dt1 0.20
  swd1 30.0
  dt2 20.0
  swd2 40.0
  rswd 70.0

# BLOCK (07)
  b 70.0
  c 140.0
  rboost 0.5
  novers 200
  djump 3.0

# BLOCK (08)
  icommrxn 5
  dind 6.0

# BLOCK (09)
  win0 1.0
  dwin 1.0
  nwin 50
  iwrec 1
  nwrec 40
  ncec 500
  rxna12f a12.rxna
  ------------------
  wbmax 20.0
  nnnos 1
  ncmx 500
  ebmin 0.0
  rmsd 2.0
  ionerun 0

# BLOCK (10)
  epfct 1.00
  ep1f ep1.grd
  ep2f ep2.grd
  qef1f 1.echa
  qef2f 2.echa

# BLOCK (11)
  edfct 1.67
  ed1f ed1.grd
  ed2f ed2.grd

# BLOCK (12)
  hdfct -0.018
  hd1f hd1.grd
  hd2f hd2.grd

# BLOCK (13)
  apfct 1.0
  napt1 0
  napt2 2
  ap2gf1 ap02-001.grd
  ap2gf2 ap02-002.grd

# BLOCK (14)
  xmin 20.0
  xmax 60.0
  ymin 20.0
  ymax 60.0
  zmin 1.5

# BLOCK (15)
  zadw 6.5
  eadw 0.13
  radw 6.0
  aadw 1.5
  ep_scale 1
  ep_scaleA 0.8
  ep_scaleB 0.39
  ep_scaleC 10.4

# BLOCK (16)
  imgch 0
  ibox 0
  iefast 0

# BLOCK (17)
  free_en 0
  free_en_z 0
  free_en_h 0.5

# BLOCK (18)
  fnintr sda.int


Detailed description of input parameters

# BLOCK 01:   dseed

# BLOCK 02 - BD trajectory parameters:   nrun, nprint, nrec, timemax

# BLOCK 03 - filenames for solute structures :   p1f, p2f

# BLOCK 04 - parameters for the description of the solution:   probep, probew, hexcl, thres

# BLOCK 05- diffusion parameters for solutes:   dm, dr, dr1, irot2f

# BLOCK 06 - Brownian motion parameters:   dt1, swd1, dt2, swd2, rswd



# BLOCK 07- parameters for dealing with protein-protein separations and close contacts:   b, c, rboost, novers, djump


# BLOCK 08- reaction criteria (some parameters are given in BLOCK 09):   icommrxn, dind

icommrxn=1 -
                        RMS average of all pairwise distances between pairs of atoms given in file rxna12f.
                        Writes complexes if  d < windows(nwrec), see BLOCK 09.

icommrxn=2 - used for association rate calculations.
                         minimum pairwise distance between pair of atoms given in files rxna12f, simultaneous occurrence is monitored for any 1, 2, 3 or 4 pairs.
                         Writes complexes if the number of contacts to define an encounter complex is equal to ncec (see BLOCK 09) AND windows is equal to win(nwrec). CAN be modifed to less than win(nwrec).

icommrxn=3 - used for association rate calculations, variant of icommrxn=2.
                         minimal pairwise distance between a pair of atoms given in file rxna12f, for independent pairs (defined by dind); simultaneous occurrence is monitored for any 1, 2, 3 or 4 pairs.
                         Writes complexes if the number of contacts to define an encounter complex is equal to ncec (see BLOCK 09) AND windows is equal to win(nwrec). CAN be modifed to less than win(nwrec).
                         Better than icommrxn=2, because it defines an encounter complex more accurately.

                          >

icommrxn=4 - used for electron transfer rate constant calculation. Files rxna1f and rxna2f (defining the reaction atom pairs) should contain pairs of atoms that may take part in an electron transfer path together with their coupling to the donor or acceptor site.  In the image below, each possible pairing (broken line) between surface atoms of proteins 1 (blue) and 2 (red) should be defined in files rxna1f and rxna2f.

icommrxn=5 - used for docking (no association rate calculation).
Accepts all configurations as encounter complexes. By using this criterion, the energetically most favorable complexes will be written to the 'complexes' file (independent of constraints).

icommrxn=6 - used for docking (no association rate calculation). Formerly icommrxn=3 in sdac.
                         Writes complexes after checking all reaction pairs  in *rxna file:
                                1: all specific pairs must be satisfied
                                2: at least nnnons (no. of independent non-specific constraints (depending on dind)) constraints must be satisfied.

icommrxn=7 - used for docking (no association rate calculation). Formerly icommrxn=2 in sdac.
                         Any non-specific constraints are considered, independence is not checked (equivalent to icommrxn=7 with dind =0, but faster).

                       

icommrxn=8 – used for docking to a surface (ibox>0, no association rate calculation).
The same as icommrxn=6, but only the vertical distance (in the z direction) is checked.

icommrxn=9 – used for docking to the surface (ibox>0, no association rate calculation).
The same as icommrxn=7, but only the vertical distance (in the z direction) is checked.

# BLOCK 09- parameters for calculation of protein kinetics (some parameters are included in BLOCK 08):   win0, dwin, nwin, iwrec, nwrec, ncec, rxna12f, nnnos, ncmx, rmsd, ionerun, wbmax, ebmin





# BLOCK 10 - parameters for electrostatic energy/forces:   epfct, ep1f, ep2f, qef1f, qef2f

# BLOCK 11 -parameters for calculation electrostatic desolvation energy/forces:   edfct, ed1f, ed2f

# BLOCK 12 -parameters for calculation of hydrophobic desolvation energy/forces:   hdfct, hd1f, hd2f

# BLOCK 13 - parameters for calculation of Lennard-Jones energy/forces:   apfct, napt1,napt2, ap1f, ap2f,ap2fg1,ap2fg2,... ap2fgx, where x=napt2

# BLOCK 14 - dimension of the simulation box for protein-surface docking, ibox>0:   xmin, xmax, ymin, ymax, zmin )

# BLOCK 15 - parameters of the hydration shell on a solid state surface (currently optimized for a Au(111) surface):   zadw, eadw, radw, aadw, ep_scale, ep_scaleA, ep_scaleB, ep_scaleC (see Kokh et al, JCTC, 2010)




# BLOCK 16- general parameters describing the symmetry of the simulation volume and the type of electrostatic calculation procedure:   ibox, imgch, iefast

# BLOCK 17 -parameters for PMF calculations (for simulation of protein docking to the solid surface only):   free_en, free_en_z, free_en_h

#BLOCK 18: monitoring of intermediate results   fnintr

Old format (used in SDA v5.01 and 4.23):

The input file consists of a series of blocks of input parameters. The format of each block of the input file is as follows:
A one (!) line description of a block of input parameters, starting with "#". On the next line, comma or space separated numerical values are given in the required order. Then, the file names (if any) are given in the required order, each on separate lines.  An example file looks like this (follow the links for detailed descriptions):

dseed = random_number_generator_seed
256.d0
#   nrun, nprint, nrec = no_of_runs, printout_every_nprint_run, record_this_run (or all runs in case of a negative nunber)
100, 5, 0
p1f, p2f = pdb_filenames_for_solute/protein_1, 2
p1.pdb
p2.pdb
#   probe, probew, hexcl, thres - probe_pr2(Å), probe_water(Å), excl_grid_spacing(Å), acc_thres(Å2)
1.70, 1.4, 0.5, 0.0
#   dm, dr, dr1, irot2f = tr_diffco, rot_diffco_2, rot_diffco_1, if_prot_1_rotates
0.027, 3.92e-5, 3.92e-5, 1
#   dt1, swd1, dt2, swd2, rswd = tstep, tstep_sw_dist_1, tstep_2, tstep_sw_dist_2, rot_sw_dist
0.50, 50.0, 20.0, 90.0, 90.0
b, c, rboost, novers, djump = b, c, boost_val, no_overs_bef_boost, jump_thr_to_rec
100.0, 500.0, 1.0,  150, 5.0
icommrxn, dind = reaction_mon_switch, force_switch, indep_dist
3, 6.0
win0, dwin, nwin, iwrec, nwrec, ncec, rxna12f = rxn_defs, rxn_at_files_prot_1, 2
1.0, 1.0, 50, 1,  40, 500
p12.rxna
epfct, ep1f, ep2f, qef1f, qef2f = e-pot_factor, e-pot_for_prot_1, 2, charges_for_prot_1, 2
1.00
ep1.grd
ep2.grd
p1.echa
p2.echa
edfct, ed1f, ed2f = e-deso_factor, e-deso_file_for_prot_1, 2
1.00
ed1.grd
ed2.grd
hdfct, hd1f, hd2f = h-deso_factor, skin, h-deso_file_for_prot_1,2
1.00
hd1.grd
hd2.grd
#   fnintr = intermediate results filename
sda.int


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

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