! read_param.cns
!     Reads parameter files.
!
! ***********************************************************************
! * Copyright 2003-2022 Alexandre Bonvin, Utrecht University.           *
!! * All rights reserved.                                                *
! * This code is part of the HADDOCK software and governed by its       *
! * license. Please see the LICENSE file that should have been included *
! * as part of this package.                                            *
! ***********************************************************************

{* protein parameter file *}
eval ($prot_parameter_infile="TOPPAR:protein-allhdg5-4.param")

{* protein CG Martini 2.2 parameter file *}
eval ($protcg_parameter_infile="TOPPAR:protein-CG-Martini-2-2.param")

{* nucleic acid parameter file *}
eval ($nucl_parameter_infile="TOPPAR:dna-rna-allatom-hj-opls-1.3.param")

{* nucleic acid CG Martini 2.1 parameter file *}
eval ($nuclcg_parameter_infile="TOPPAR:dna-rna-CG-MARTINI-2-1p.param")

{* carbohydrate parameter file *}
eval ($carbo_parameter_infile="TOPPAR:carbohydrate.param")

{* solvent parameter file *}
eval ($solv_parameter_infile="TOPPAR:solvent-allhdg5-4.param")

{* fragment probes parameter file *}
eval ($ligands_parameter_infile="TOPPAR:fragment_probes.param")

{* ion parameter file *}
eval ($ion_parameter_infile="TOPPAR:ion.param")

{* heme parameter file *}
eval ($heme_parameter_infile="TOPPAR:hemes-allhdg.param")

{* shape parameter file *}
eval ($shape_parameter_infile="TOPPAR:shape.param")

{* cofactors parameter file *}
eval ($cofactors_parameter_infile="TOPPAR:cofactors.param")


! check for the presence of a CG model
do (store4 = 0) (all)
do (store4 = 1) (name BB or name BB#)
show sum (store4) (all)
if ($result > 0) then
    eval ($cgmodel = true)
else
    eval ($cgmodel = false)
end if


parameter
    @@$prot_parameter_infile
    @@$ion_parameter_infile
    @@$nucl_parameter_infile
    @@$carbo_parameter_infile
    @@$solv_parameter_infile
    @@$ligands_parameter_infile
    @@$heme_parameter_infile
    @@$shape_parameter_infile
    @@$cofactors_parameter_infile
    if ($ligand_param_fname # "") then 
        fileexist $ligand_param_fname end
        if ($result eq true) then
            @@$ligand_param_fname
        end if
    end if
    if ($cgmodel eq true) then
        @@$protcg_parameter_infile
        @@$nuclcg_parameter_infile
    end if
end

parameter
    nbonds
        nbxmod=5 atom cdie shift
        cutnb=9.5 ctofnb=8.5 ctonnb=6.5 eps=1.0 e14fac=0.4 inhibit 0.25
        wmin=0.5 tolerance  0.5
    end
end

igroup
  interaction  (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA))
               (not (resn ANI or resn DAN or resn XAN or resn DUM or resn SHA)) weight * 1 end
  interaction  (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM)
               (resn ANI or resn DAN or resn XAN or resn DUM or resn DUM) weight * 1 vdw 0.0 elec 0.0 end
  interaction  (resn SHA) (not resn SHA) weight * 0 end

end

inline @MODULE:charge-beads-interactions.cns