read_pdb.f90 File Reference

Functions/Subroutines
subroutine	read_pdb (pdb_filename, rcriter, tmp_atom_letter, tmp_atom_position, tmp_rcriter_pos, counter_prot)
	Read the PDB file. More...

Detailed Description

Version

{version 7.2.3 (2019)}

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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

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Subroutine read_pdb()

Function/Subroutine Documentation

read_pdb()

subroutine read_pdb	(	character*128	pdb_filename,
		type ( react_criter )	rcriter,
		character*2, dimension(:), intent(inout), pointer	tmp_atom_letter,
		real ( kind=8 ), dimension(:,:), intent(inout), pointer	tmp_atom_position,
		real ( kind=8 ), dimension(:,:), intent(inout), pointer	tmp_rcriter_pos,
		integer, intent(in)	counter_prot
	)

Read the PDB file.

Read position of atoms, they are only temporary data. Only the accessible atoms are later used
Add array tmp_rcriter_pos, if associated will be used for updating position of reaction criteria if the protein is flexible
Read hexadecimal number if present (VMD and more than 100000 atoms)

Parameters

pdb_filename	: name of the file
rcriter	: instance of react_criter
tmp_atom_letter	used later for Van der Walls
tmp_atom_position	position of all atoms in pdb
tmp_rcriter_pos	: position of the reaction criteria
counter_prot	: protein id, used for reaction criteria

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