SDA  7.1
Simulation of Diffusional Association
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Functions/Subroutines
prepare_grid.f90 File Reference

Load the grids and call prepare_atom_protein. More...

Functions/Subroutines

subroutine prepare_grid (pdb_filename, q_filename, ep_filename, ed_filename, hd_filename, lj_rep_filename, lj_filename, atom_type_name, epfct, edfct, hdfct, lj_rep_fct, ljfct, param_analytic, dm, dr, stoke_rad, param_probe, bool_excl_grid, psgrid, center, counter_grid, counter_conf, rcriter, iflex, isurface, type_calc, nb_lj_opt)
 Allocate one set of grid and return an associated pointer on it. More...
 

Detailed Description

Load the grids and call prepare_atom_protein.

Version
{version 7.1 (2015)}

Copyright (c) 2009, 2010, 2015 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) formerly EML Research gGmbH (EML-R ) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Copyright (c) 2000, 2003 European Molecular Biology Laboratory Meyerhofstr. 1, Postfach 10.2209 D-69012, Heidelberg, Germany

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References (see also http://mcm.h-its.org/sda7/doc/doc_sda7/references.html):

Brownian dynamics simulation of protein-protein diffusional encounter.

(1998) Methods, 14, 329-341.

Authors: M.Martinez, N.J.Bruce, J.Romanowska, D.B.Kokh, P.Mereghetti, R.R.Gabdoulline, M. Ozboyaci, S.Richter and R.C.Wade


Function/Subroutine Documentation

subroutine prepare_grid ( character*128, intent(in)  pdb_filename,
character*128, intent(in)  q_filename,
character*128, intent(in)  ep_filename,
character*128, intent(in)  ed_filename,
character*128, intent(in)  hd_filename,
character*128, intent(in)  lj_rep_filename,
character*128, dimension(:), intent(in), allocatable  lj_filename,
character*2, dimension(:), intent(in), allocatable  atom_type_name,
real ( kind=8 ), intent(in)  epfct,
real ( kind=8 ), intent(in)  edfct,
real ( kind=8 ), intent(in)  hdfct,
real ( kind=8 ), intent(in)  lj_rep_fct,
real ( kind=8 ), intent(in)  ljfct,
type ( parameter_analytic )  param_analytic,
real ( kind=8 ), intent(in)  dm,
real ( kind=8 ), intent(in)  dr,
real ( kind=8 ), intent(in)  stoke_rad,
type ( probe_type )  param_probe,
logical  bool_excl_grid,
type ( sogrid ), pointer  psgrid,
real ( kind=8 ), dimension( 3 )  center,
integer, intent(in)  counter_grid,
integer, intent(in)  counter_conf,
type ( react_criter )  rcriter,
logical  iflex,
logical  isurface,
type ( type_calculation )  type_calc,
integer, optional  nb_lj_opt 
)

Allocate one set of grid and return an associated pointer on it.

Group all allocation for set of grids, call prepare_atom_protein to load the pdbs and charges
The initialisation of sogrid must be done before
Correctly read position of reaction coordinate ( in case of flex )
Add iflex, if THIS Solute_Grid group is not flexible, assign criteria pos from rxna ( default counter for id 1 or 2 ) If Flex, read new coordinate in tmp_atom_rcriteria, to not erase pos from rxna

Parameters
pdb_filename: name of the pdb
q_filename,ep_filename,ed_filename,hd_filename,lj_rep_filename,lj_filename: name of the charge and grids
atom_type_name: atom to use for lennard-jones interaction
epfct,edfct,hdfct,lj_rep_fct,ljfct: multiplicative factors for the grids
param_analytic: structure parameter_analytic
dm,dr: translational and rotational coefficient diffusion
stoke_rad: stoke_radius for hydrodynamic interactions
param_probe: contains the different probe in param_probe
bool_excl_grid: if the exclusion grid must be computed ( or read from the disk )
psgrid: pointer to sogrid to fill
center: center of the protein
counter_grid,counter_conf: internal counters
rcriter: instance of react_criter
iflex: if the solute is flexible
isurface: if the surface is a surface
type_calc: instance of type_calculation
nb_lj_opt: optional number of lennard-jones grid or atom type to read

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