check_exclusion.f90 File Reference

Check if protein 2 overlaps with protein 1
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Functions/Subroutines
subroutine	check_exclusion (prot1, prot2, rtry, rot_try, overlap, do_rot)
	Check exclusion with dynamic exclusion grid Only check protein 2 in exclusion grid of protein 1, default in sda As soon a first overlap is found, we exit from the function The new position and new orientation are tested to check if there is an overlap. New position are not applied to the solute in this function, because a serie of transformation will be applied at the end. Maybe not the best method.

Detailed Description

Check if protein 2 overlaps with protein 1
.

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

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Only for sda_2proteins and related. Sdamm implements a repulsive lennard-jones interaction

Function/Subroutine Documentation

check_exclusion()

subroutine check_exclusion	(	type ( protein ), intent(in), target	prot1,
		type ( protein ), intent(in), target	prot2,
		real ( kind=8 ), dimension (3), intent(in)	rtry,
		real ( kind=8 ), dimension (3,3), intent(in)	rot_try,
		logical, intent(out)	overlap,
		logical, intent(in)	do_rot
	)

Check exclusion with dynamic exclusion grid
Only check protein 2 in exclusion grid of protein 1, default in sda
As soon a first overlap is found, we exit from the function
The new position and new orientation are tested to check if there is an overlap.
New position are not applied to the solute in this function, because a serie of transformation will be applied at the end.
Maybe not the best method.

Parameters

prot1	: solute 1
prot2	: solute 2
rtry	: new position of the protein to check
rot_try	: new orientation of the protein to check
overlap	: true if the move is rejected
do_rot	: indicates if the rotation need to be applied

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