trajectory2dcd.f90 File Reference

Functions/Subroutines
program	trajectory2dcd
	Program trajectory2dcdRead record (complexes or trajectory file ) and convert to pdb / dcd files Support sda_2proteins / sdamm with flexible solutes. More...
subroutine	open_dcd_file (filename, ioutf, nb_atoms, nb_frames)
	Open file and write the header. More...
subroutine	write_dcd (tab_prot, ioutf, nat, cm)
	Write data into the dcd file. More...
subroutine	write_dcd_all_conf (tab_prot, ioutf, nat, cm, conf_number)
	Version to call if change of conformation with variable number of atoms. More...
subroutine	generate_pdb (tab_prot, filename, all_filename_pdb, cm, force_all_conf)
	Write pdb files. More...
subroutine	copy_pdb (prot, filename_pdb, pdb_out_int, cm, max_size, bool_extend)
	Copy one pdb file into an other. More...
subroutine	copy_all_pdbs (prot, all_filename_pdb, pdb_out_int)
	Copy pdb files for every conformations. More...

Detailed Description

Version

{version 7.2.3 (2019)}

Copyright (c) 2009, 2010, 2015, 2016, 2019 Heidelberg Institute of Theoretical Studies (HITS, www.h-its.org) Schloss-Wolfsbrunnenweg 35 69118 Heidelberg, Germany

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, 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

---

Convert record into pdb or dcd file

Function/Subroutine Documentation

copy_all_pdbs()

subroutine copy_all_pdbs	(	type ( protein )	prot,
		character*64, dimension(:,:)	all_filename_pdb,
		integer	pdb_out_int
	)

Copy pdb files for every conformations.

Copy lines by lines into pdb_out

Parameters

prot	: instance of protein
all_filename_pdb	: name of all conformations
pdb_out_int	: file descriptor of the target pdb file

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copy_pdb()

subroutine copy_pdb	(	type ( protein )	prot,
		character*64	filename_pdb,
		integer	pdb_out_int,
		real ( kind = 8 ), dimension ( 3 )	cm,
		integer	max_size,
		logical	bool_extend
	)

Copy one pdb file into an other.

Copy lines by lines
Used if gen_conf, will read lines from pdb_in and copy to pdb_out

Parameters

prot	: instance of protein
filename_pdb	: name of the pdb file
pdb_out_int	: file descriptor of the target pdb file
cm	: center of geometry of the second solute ( only sda_2proteins )
max_size	: maximum number of atoms
bool_extend	: if true, all output will have the maximum size

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generate_pdb()

subroutine generate_pdb	(	type ( array_protein_type )	tab_prot,
		character*64	filename,
		character*64, dimension(:,:)	all_filename_pdb,
		real ( kind = 8 ), dimension ( 3 )	cm,
		logical	force_all_conf
	)

Write pdb files.

Parameters

tab_prot	: instance of array_protein_type
filename	: name of the pdb file to write
all_filename_pdb	:
cm	: center of geometry, only needed for sda_2proteins. send (0,0,0) otherwise
force_all_conf	: force to write all conformations

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open_dcd_file()

subroutine open_dcd_file	(	character*40, intent(in)	filename,
		integer	ioutf,
		integer	nb_atoms,
		integer	nb_frames
	)

Open file and write the header.

try to separate dcd format, may be a module if used more

Parameters

filename	: file to create
ioutf	: file descriptor of the file to open
nb_atoms	: total number of atoms
nb_frames	: number of frames

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write_dcd()

subroutine write_dcd	(	type ( array_protein_type )	tab_prot,
		integer	ioutf,
		integer	nat,
		real ( kind = 8 ), dimension ( 3 )	cm
	)

Write data into the dcd file.

Parameters

tab_prot	: instance of array_protein_type
ioutf	: file descriptor of the dcd file
nat	: number of atoms
cm	: center of geometry, only needed for sda_2proteins. send (0,0,0) otherwise

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write_dcd_all_conf()

subroutine write_dcd_all_conf	(	type ( array_protein_type )	tab_prot,
		integer	ioutf,
		integer	nat,
		real ( kind = 8 ), dimension ( 3 )	cm,
		integer	conf_number
	)

Version to call if change of conformation with variable number of atoms.

Experimental : write all conformation at once
need to print all x first, then all y and all z, need to test all size inside

Parameters

tab_prot	: instance of array_protein_type
ioutf	: file descriptor of the dcd file
nat	: number of atoms
cm	: center of geometry, only needed for sda_2proteins. send (0,0,0) otherwise
conf_number	: the conformation to print, all other will be at the exact same position

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