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

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

Functions/Subroutines

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

Detailed Description

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

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

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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_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,
type ( type_calculation )  type_calc 
)

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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