Examples
Here is a full example of the benchmark.yaml
file for both HADDOCK2.4 and HADDOCK3.0.
HADDOCK2.4
general:
executable: /workspaces/haddock-runner/haddock24.sh
max_concurrent: 2
haddock_dir: /Users/rodrigo/repos/haddock
receptor_suffix: _r_u
ligand_suffix: _l_u
input_list: /workspaces/haddock-runner/example/input_list.txt
work_dir: /workspaces/haddock-runner/bm-goes-here
scenarios:
- name: true-interface
parameters:
run_cns:
noecv: false
structures_0: 1000
structures_1: 200
waterrefine: 200
restraints:
ambig: ambig
unambig: restraint-bodies
hbonds: hbonds
custom_toppar:
topology: _ligand.top
param: _ligand.param
- name: center-of-mass
parameters:
run_cns:
cmrest: true
structures_0: 10000
structures_1: 400
waterrefine: 400
anastruc_1: 400
custom_toppar:
topology: _ligand.top
param: _ligand.param
- name: random-restraints
parameters:
run_cns:
ranair: true
structures_0: 10000
structures_1: 400
waterrefine: 400
anastruc_1: 400
custom_toppar:
topology: _ligand.top
param: _ligand.param
#-----------------------------------------------
HADDOCK3.0
general:
executable: /workspaces/haddock-runner/example/haddock3.sh
max_concurrent: 4
haddock_dir: /opt/haddock3
receptor_suffix: _r_u
ligand_suffix: _l_u
input_list: /workspaces/haddock-runner/example/input_list.txt
work_dir: /workspaces/haddock-runner/bm-goes-here
scenarios:
- name: true-interface
parameters:
general:
mode: local
ncores: 8
modules:
order:
[topoaa, rigidbody, seletop, flexref, emref, clustfcc, seletopclusts]
topoaa:
autohis: true
rigidbody:
ambig_fname: _ambig.tbl
unambig_fname: _restraint-bodies.tbl
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
seletop:
select: 200
flexref:
ambig_fname: _ambig.tbl
unambig_fname: _restraint-bodies.tbl
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
emref:
ambig_fname: _ambig
clustfcc:
seletopclusts:
- name: center-of-mass
parameters:
general:
mode: local
ncores: 8
modules:
order:
[topoaa, rigidbody, seletop, flexref, emref, clustfcc, seletopclusts]
topoaa:
autohis: true
rigidbody:
sampling: 10000
cmrest: true
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
seletop:
select: 400
flexref:
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
emref:
clustfcc:
seletopclusts:
- name: random-restraints
parameters:
general:
mode: local
ncores: 8
modules:
order:
[topoaa, rigidbody, seletop, flexref, emref, clustfcc, seletopclusts]
topoaa:
autohis: true
rigidbody:
sampling: 10000
ranair: true
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
seletop:
select: 400
flexref:
contactairs: true
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
emref:
contactairs: true
ligand_param_fname: _ligand.param
ligand_top_fname: _ligand.top
clustfcc:
seletopclusts:
#-----------------------------------------------