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... | |
Load the grids and call prepare_atom_protein.
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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
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
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 |