| ! 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 |
|
|
