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... | |
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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
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
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 |