SDA (SDA flex)  7.2
Simulation of Diffusional Association
Functions/Subroutines
prepare_atom_protein.f90 File Reference

Functions/Subroutines

subroutine prepare_atom_protein (sgrid, rcriter, pdb_filename, param_probe, center, counter, bool_excl_grid, iflex, isurface, vert_excl, type_calc, fixed_cent_opt)
 Read pdb file, assign vdw radius and compute atom_surface, exclusion grid if needed and setup the reaction criteria. More...
 

Detailed Description

Version
{version 7.2.3 (2019)}

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References: see also http://mcm.h-its.org/sda7/do:c/doc_sda7/references.html:

Brownian dynamics simulation of protein-protein diffusional encounter. (1998) Methods, 14, 329-341.

SDA 7: A modular and parallel implementation of the simulation of diffusional association software. Journal of computational chemistry 36.21 (2015): 1631-1645.

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


call by prepare_grid.f90 for setting atom position and exclusion grid

Function/Subroutine Documentation

◆ prepare_atom_protein()

subroutine prepare_atom_protein ( type ( sogrid sgrid,
type ( react_criter rcriter,
character ( 128 ), intent(in)  pdb_filename,
type ( probe_type ), intent(in)  param_probe,
real ( kind=8 ), dimension(3), intent(out)  center,
integer  counter,
logical, intent(in)  bool_excl_grid,
logical, intent(in)  iflex,
logical, intent(in)  isurface,
logical, intent(in)  vert_excl,
type ( type_calculation type_calc,
real ( kind=8 ), dimension(3), intent(in), optional  fixed_cent_opt 
)

Read pdb file, assign vdw radius and compute atom_surface, exclusion grid if needed and setup the reaction criteria.

Assign all the data to a set_of_grid, not to proteins
Should be called only by prepare_grid ( never grid without pdbs, flex : each grid a pdb ), simple to handle
Log file for printing of eclusion.log and reaction criteria.log
Check if the accessibility file and/or the exclusion grid has already been computed. In this case the pdb does not need to be read again

Parameters
sgrid: instance of sogrid
rcriter: instance of react_criter
pdb_filename:
param_probe: contains the different probe in param_probe
center: return the center of the solutes
counter: internal counter
bool_excl_grid: if exclusion grid is needed ( solute 1 in sda_2proteins )
iflex: if the solute is flexible
isurface: if the solute is a surface
type_calc: instance of type_calculation
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