prepare_atom_protein.f90 File Reference

Functions/Subroutines
subroutine	prepare_atom_protein (sgrid, rcriter, pdb_filename, sasa_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.

Detailed Description

Version

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

Please send your contact address to get information on updates and new features to "mcmsoft@h-its.org". Questions will be answered as soon as possible.

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,
		character ( 128 ), intent(in)	sasa_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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