SDA  7.1
Simulation of Diffusional Association
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Functions/Subroutines
read_pdb.f90 File Reference

Subroutine read_pdb() More...

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

Subroutine read_pdb()

Version
{version 7.1 (2015)}

Copyright (c) 2009, 2010, 2015 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) formerly EML Research gGmbH (EML-R ) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

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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


Function/Subroutine Documentation

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_letterused later for Van der Walls
tmp_atom_positionposition 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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