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SDA (SDA flex)
7.2
Simulation of Diffusional Association
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SDA (SDA flex)
7.2
Simulation of Diffusional Association
|
Functions/Subroutines | |
| subroutine | prepare_grid (pdb_filename, sasa_filename, q_filename, ep_filename, ed_filename, hd_filename, lj_rep_filename, lj_filename, atom_type_name, epfct, edfct, hdfct, lj_rep_fct, ljfct, epfct_oneway_surf, param_analytic, dm, dr, dh_rad, vol_rad, rep_rad, param_probe, bool_excl_grid, psgrid, center, counter_grid, counter_conf, rcriter, iflex, isurface, isphere_crowd, ishape_crowd, ioneway, vert_excl, type_calc, iimg_chg, real_net_charge, surface_charge_dens, fixed_cent, intenergy, conf_weight, nb_lj_opt) |
| Allocate one set of grid and return an associated pointer on it. | |
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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, A.Muñiz-Chicharro, R.Beccaria 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
Load the grids and call prepare_atom_protein
| subroutine prepare_grid | ( | character*128, intent(in) | pdb_filename, |
| character*128, intent(in) | sasa_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, | ||
| real ( kind=8 ), intent(in) | epfct_oneway_surf, | ||
| type ( parameter_analytic ) | param_analytic, | ||
| real ( kind=8 ), intent(in) | dm, | ||
| real ( kind=8 ), intent(in) | dr, | ||
| real ( kind=8 ), intent(in) | dh_rad, | ||
| real ( kind=8 ), intent(in) | vol_rad, | ||
| real ( kind=8 ), intent(in) | rep_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, | ||
| logical | isphere_crowd, | ||
| logical | ishape_crowd, | ||
| logical | ioneway, | ||
| logical, intent(in) | vert_excl, | ||
| type ( type_calculation ) | type_calc, | ||
| logical, intent(in) | iimg_chg, | ||
| real ( kind=8 ), intent(in) | real_net_charge, | ||
| real ( kind=8 ), intent(in) | surface_charge_dens, | ||
| real ( kind=8 ), dimension( 3 ), intent(in) | fixed_cent, | ||
| logical, intent(in) | intenergy, | ||
| real(kind=8), intent(in) | conf_weight, | ||
| 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 |
| dh_rad | : radius used in Debye Hueckel interaction terms to define solute cavity |
| vol_rad | : radius used in hydrodynamic calculations to define occupied volumes |
| rep_rad | : radius used in defining soft-core repulsion in spherical crowder model |
| 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 |
| vert_excl | : when performing excluded volume checks, is rhit considered in vertical (ie z ) direction only |
| type_calc | : instance of type_calculation |
| fixed_cent | : for a surface, the centre position can be set in input, rather than from geometric centre |
| nb_lj_opt | : optional number of lennard-jones grid or atom type to read @isphere_crowd : boolean, indicates if a crowder is spherical @ishape_crowd : boolean, indicates if a crowder has a different shape from spherical (not implemented yet) @intEnergy : boolean, indicates whether internal energy is used @conf_weight : real, conformation weight |
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