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bis-aria
ariaec
Commits
1b9fa481
Commit
1b9fa481
authored
Dec 20, 2018
by
Fabrice Allain
Browse files
feat: add v2.3.7 aria project template
parent
39d1d475
Changes
2
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aria/conbox/conf/config.ini
View file @
1b9fa481
...
...
@@ -184,6 +184,15 @@ logharmonic_potential_weight_hbond: 25.0
rama_potential_enabled:
yes
hbdb_potential_enabled:
no
scoring_method:
standard
md_parameters_dynamics:
torsion
md_parameters_tad_temp_high:
10000.0
md_parameters_tad_timestep_factor:
9.0
md_parameters_cartesian_temp_high:
2000.0
md_parameters_cartesian_first_iteration:
0
md_parameters_timestep:
0.003
md_parameters_temp_cool1_final:
1000.0
md_parameters_temp_cool2_final:
50.0
md_parameters_steps_refine:
4000
md_parameters_random_seed:
89764443
md_parameters_steps_high:
10000
md_parameters_steps_cool1:
5000
...
...
aria/conbox/templates/aria_project_v2.3.7.xml
0 → 100644
View file @
1b9fa481
<!-- Template with method field in clustering tag -->
<!DOCTYPE project SYSTEM "project1.0.dtd">
<project
name=
"${project_name}"
version=
"1.0"
author=
""
date=
"${date}"
description=
""
comment=
""
references=
""
working_directory=
"${working_directory}"
temp_root=
"${temp_root}"
run=
"${runid}"
file_root=
"${file_root}"
cache=
"yes"
cleanup=
"yes"
>
<data>
<ccpn_model
filename=
""
/>
<molecule
file=
"${molecule_file}"
format=
"xml"
ccpn_id=
""
>
<linkage_definition
name=
"automatic"
filename=
""
/>
<parameter_definition
name=
"${parameter_definition}"
filename=
""
/>
<topology_definition
name=
"automatic"
filename=
""
/>
</molecule>
% if unambiguous_distance_restraints:
% for unambig_id in unambiguous_distance_restraints:
<unambiguous_distance_restraints
file=
"${unambiguous_distance_restraints[unambig_id]['file']}"
format=
"${unambiguous_distance_restraints[unambig_id]['format']}"
ccpn_id=
"${unambiguous_distance_restraints[unambig_id]['ccpn_id']}"
enabled=
"${unambiguous_distance_restraints[unambig_id]['enabled']}"
add_to_network=
"${unambiguous_distance_restraints[unambig_id]['add_to_network']}"
calibrate=
"${unambiguous_distance_restraints[unambig_id]['calibrate']}"
run_network_anchoring=
"${unambiguous_distance_restraints[unambig_id]['run_network_anchoring']}"
filter_contributions=
"${unambiguous_distance_restraints[unambig_id]['filter_contributions']}"
/>
% endfor
% endif
% if ambiguous_distance_restraints:
% for ambig_id in ambiguous_distance_restraints:
<ambiguous_distance_restraints
file=
"${ambiguous_distance_restraints[ambig_id]['file']}"
format=
"${ambiguous_distance_restraints[ambig_id]['format']}"
ccpn_id=
"${ambiguous_distance_restraints[ambig_id]['ccpn_id']}"
enabled=
"${ambiguous_distance_restraints[ambig_id]['enabled']}"
add_to_network=
"${ambiguous_distance_restraints[ambig_id]['add_to_network']}"
calibrate=
"${ambiguous_distance_restraints[ambig_id]['calibrate']}"
run_network_anchoring=
"${ambiguous_distance_restraints[ambig_id]['run_network_anchoring']}"
filter_contributions=
"${ambiguous_distance_restraints[ambig_id]['filter_contributions']}"
avg_exponent=
"${ambiguous_distance_restraints[ambig_id]['avg_exponent']}"
/>
% endfor
% endif
% if hbond_dist_file:
<hbonds
file=
"${hbond_dist_file}"
format=
"tbl"
ccpn_id=
""
enabled=
"yes"
data_type=
"standard"
/>
% endif
% if dihed_angle_file:
<dihedrals
file=
"${dihed_angle_file}"
format=
"tbl"
ccpn_id=
""
enabled=
"yes"
data_type=
"standard"
/>
% endif
<symmetry
enabled=
"no"
method=
"standard"
n_monomers=
"1"
symmetry_type=
"None"
ncs_enabled=
"no"
packing_enabled=
"no"
/>
<initial_structure
file=
""
format=
"iupac"
ccpn_id=
""
enabled=
"no"
/>
</data>
<structure_generation
engine=
"cns"
>
<cns
local_executable=
"${cns_executable}"
keep_output=
"${cns_keep_output}"
keep_restraint_files=
"yes"
create_psf_file=
"yes"
generate_template=
"yes"
nonbonded_parameters=
"PROLSQ"
>
<annealing_parameters>
<unambiguous_restraints
first_iteration=
"0"
k_hot=
"10.0"
k_cool1_initial=
"${unambiguous_restraints_k_cool1_initial}"
k_cool1_final=
"${unambiguous_restraints_k_cool1_final}"
k_cool2=
"${unambiguous_restraints_k_cool2}"
/>
<ambiguous_restraints
first_iteration=
"0"
k_hot=
"10.0"
k_cool1_initial=
"10.0"
k_cool1_final=
"50.0"
k_cool2=
"50.0"
/>
<hbond_restraints
first_iteration=
"0"
k_hot=
"10.0"
k_cool1_initial=
"${hbond_restraints_k_cool1_initial}"
k_cool1_final=
"${hbond_restraints_k_cool1_final}"
k_cool2=
"${hbond_restraints_k_cool2}"
/>
<dihedral_restraints
k_hot=
"5.0"
k_cool1=
"${dihedral_restraints_k_cool1}"
k_cool2=
"${dihedral_restraints_k_cool2}"
/>
<karplus_restraints
parameter_class=
"1"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"2"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"3"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"4"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<karplus_restraints
parameter_class=
"5"
a=
"6.98"
b=
"-1.38"
c=
"1.72"
d=
"-60.0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
/>
<rdc_restraints
parameter_class=
"1"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"2"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"3"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"4"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<rdc_restraints
parameter_class=
"5"
method=
"SANI"
first_iteration=
"0"
k_hot=
"0.0"
k_cool1=
"0.2"
k_cool2=
"1.0"
r=
"0.4"
d=
"8.0"
border_hot_initial=
"0.1"
border_hot_final=
"40.0"
border_cool1_initial=
"40.0"
border_cool1_final=
"40.0"
border_cool2_initial=
"40.0"
border_cool2_final=
"40.0"
center_hot_initial=
"0.1"
center_hot_final=
"0.1"
center_cool1_initial=
"10.0"
center_cool1_final=
"10.0"
center_cool2_initial=
"10.0"
center_cool2_final=
"10.0"
/>
<flat_bottom_harmonic_wall
m_rswitch_hot=
"0.5"
m_rswitch_cool1=
"0.5"
m_rswitch_cool2=
"0.5"
rswitch_hot=
"0.5"
rswitch_cool1=
"0.5"
rswitch_cool2=
"0.5"
m_asymptote_hot=
"-1.0"
m_asymptote_cool1=
"-1.0"
m_asymptote_cool2=
"-0.1"
asymptote_hot=
"1.0"
asymptote_cool1=
"1.0"
asymptote_cool2=
"0.1"
/>
<symmetry_restraints
k_packing_hot=
"15.0"
k_packing_cool1=
"10.0"
k_packing_cool2=
"5.0"
last_iteration_packing=
"8"
k_ncs=
"50.0"
/>
<logharmonic_potential
enabled=
"${logharmonic_potential_enabled}"
use_auto_weight=
"${logharmonic_potential_use_auto_weight}"
weight_unambig=
"${logharmonic_potential_weight_unambig}"
weight_ambig=
"${logharmonic_potential_weight_ambig}"
weight_hbond=
"${logharmonic_potential_weight_hbond}"
/>
<rama_potential
enabled=
"${rama_potential_enabled}"
weight_rama=
"1.0"
/>
<hbdb_potential
enabled=
"${hbdb_potential_enabled}"
/>
<scoring
method=
"${scoring_method}"
/>
</annealing_parameters>
<md_parameters
dynamics=
"${}"
random_seed=
"${md_parameters_random_seed}"
tad_temp_high=
"${}"
tad_timestep_factor=
"${}"
cartesian_temp_high=
"${}"
cartesian_first_iteration=
"${}"
timestep=
"${}"
temp_cool1_final=
"${}"
temp_cool2_final=
"${}"
steps_high=
"${md_parameters_steps_high}"
steps_refine=
"${}"
steps_cool1=
"${md_parameters_steps_cool1}"
steps_cool2=
"${md_parameters_steps_cool2}"
/>
</cns>
<job_manager
default_command=
"csh -f"
>
<host
enabled=
"yes"
command=
"${host_command}"
executable=
"${host_executable}"
n_cpu=
"${n_cpus}"
use_absolute_path=
"yes"
/>
</job_manager>
</structure_generation>
<protocol
floating_assignment=
"yes"
>
% for iter in range(0, int(iterations + 1)):
<iteration
number=
"${iter}"
n_structures=
"${iteration_n_structures}"
sort_criterion=
"${iteration_sort_criterion}"
n_best_structures=
"${iteration_n_best_structures}"
n_kept_structures=
"${iteration_n_kept_structures}"
>
<assignment/>
<merging
method=
"${merging_method}"
/>
<calibration
relaxation_matrix=
"${calib_relaxation_matrix}"
distance_cutoff=
"${calib_distance_cutoff}"
estimator=
"${calib_estimator}"
error_estimator=
"${calib_error_estimator}"
/>
<violation_analysis
violation_tolerance=
"${viol_violation_tolerance[iter]}"
violation_threshold=
"${viol_violation_threshold}"
sigma_mode=
"${viol_sigma_mode}"
/>
<partial_assignment
weight_threshold=
"${partassign_weight_threshold[iter]}"
max_contributions=
"${partassign_max_contributions}"
exponent=
"${partassign_exponent}"
/>
<network_anchoring
high_residue_threshold=
"${netanch_high_residue_threshold}"
enabled=
"${netanch_enabled}"
min_residue_threshold=
"${netanch_min_residue_threshold}"
min_atom_threshold=
"${netanch_min_atom_threshold}"
/>
<clustering
enabled=
"${clustering_enabled}"
mask=
"${clustering_mask}"
n_clusters=
"${clustering_nclusters}"
method=
"${clustering_method}"
/>
</iteration>
% endfor
<water_refinement
solvent=
"${water_refinement_solvent}"
n_structures=
"${water_refinement_n_structures}"
enabled=
"${water_refinement_enabled}"
write_solvent_molecules=
"${water_refinement_write_solvent_molecules}"
/>
</protocol>
<analysis>
<structures_analysis
enabled=
"yes"
/>
<procheck
executable=
"${procheck_executable}"
enabled=
"${procheck_enabled}"
/>
<prosa
executable=
"${prosa_executable}"
enabled=
"${prosa_enabled}"
/>
<whatif
executable=
"${whatif_executable}"
enabled=
"${whatif_enabled}"
/>
<clashlist
executable=
"${clashlist_executable}"
enabled=
"${clahlist_enabled}"
/>
</analysis>
<report>
<ccpn
export_assignments=
"no"
export_noe_restraint_list=
"no"
export_structures=
"no"
/>
<molmol
enabled=
"yes"
/>
<noe_restraint_list
pickle_output=
"${pickle_output}"
text_output=
"yes"
xml_output=
"no"
/>
<spectra
write_assigned=
"no"
write_assigned_force=
"no"
iteration=
"last"
write_unambiguous_only=
"yes"
/>
</report>
</project>
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