diff --git a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml index 2c347f4..798cca9 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml @@ -1598,6 +1598,200 @@ nodes: elecflag: ui:group: force field tomlSchema: {} +- id: openmm + category: refinement + label: OpenMM refinement module for HADDOCK3. + description: HADDOCK3 OpenMM module. + schema: + type: object + properties: + forcefield: + default: amber14-all.xml + title: Forcefield used by OpenMM. + description: Forcefields that can be used by OpenMM. + $comment: Forcefields that can be used by OpenMM. + type: string + minLength: 10 + maxLength: 100 + enum: + - amber14-all.xml + - amber14/protein.ff14SB.xml + - amber14/protein.ff15ipq.xml + - amber14/DNA.OL15.xml + - amber14/DNA.bsc1.xml + - amber14/RNA.OL3.xml + - amber14/lipid17.xml + - amber14/GLYCAM_06j-1.xml + - charmm36.xml + explicit_solvent_model: + default: amber14/tip3p.xml + title: Explicit solvent models. + description: Solvent models supported by the OpenMM modeller to build the + water solvation box. + $comment: Solvent models supported by the OpenMM modeller to build the water + solvation box. + type: string + minLength: 0 + maxLength: 100 + enum: + - amber14/tip3p.xml + - amber14/spce.xml + - charmm36/spce.xml + - amber14/tip4pew.xml + - charmm36/tip4pew.xml + - charmm36/tip5p.xml + keep_solvent: + default: false + title: Whether-or-not solvent be removed from provided structures. + description: Whether-or-not solvent be removed from provided structures. + $comment: Whether-or-not solvent be removed from provided structures. If 'false', + all HETATM atoms will be removed. + type: boolean + implicit_solvent: + default: false + title: Indicate use of implicit solvent. + description: Indicate use of implicit solvent, avoids building a water solvation + box around pdbs. + $comment: Indicate use of implicit solvent, avoids building a water solvation + box around pdbs. + type: boolean + implicit_solvent_model: + default: implicit/hct.xml + title: Implicit solvent models. + description: Implicit solvent models supported by OpenMM. + $comment: Implicit solvent models supported by OpenMM. + type: string + minLength: 0 + maxLength: 100 + enum: + - implicit/hct.xml + - implicit/obc1.xml + - implicit/obc2.xml + - implicit/gbn.xml + - implicit/gbn2.xml + add_extra_particles_for_forcefield: + default: false + title: Add extra particles for forcefield. + description: Add extra particles for forcefield if needed such as e.g. Drude + particles. + $comment: Add extra particles for forcefield if needed such as e.g. Drude + particles. + type: boolean + constraints: + default: HBonds + title: Integration constraints. + description: Integration constraints used to allow for larger integration + time step. + $comment: Integration constraints used to allow for larger integration time + step. For extra info see http://docs.openmm.org/latest/userguide/application/02_running_sims.html#constraints + type: string + minLength: 1 + maxLength: 20 + enum: + - None + - HBonds + - AllBonds + - HAngles + sampling_factor: + default: 1 + title: Number of simulation replicas. + description: Number of simulation replicas. + $comment: Number of simulation replicas. + type: number + maximum: 20 + minimum: 1 + temperature_kelvin: + default: 298.15 + title: Average temperature. + description: Average temperature used by e.g. the integrator or by for temperature + coupling. + $comment: Average temperature used by e.g. the integrator or by for temperature + coupling. + type: number + maximum: 1000.0 + minimum: 1.0 + remove_center_of_mass_motion: + default: true + title: Remove center of mass motion. + description: Remove center of mass motion when overall molecular drift is + detected. + $comment: Remove center of mass motion when overall molecular drift is detected. + type: boolean + generate_ensemble: + default: true + title: Generate ensemble of configurations. + description: Generate ensemble of configurations. + $comment: If 'true', generates 1 single ensemble .pdb file holding various + configurations; composed of the equilibrated one, all intermediates and + the final one. If 'false', only return the last configuration obtained after + 'simulation_timesteps' steps. + type: boolean + rigid_water: + default: true + title: Use rigid water. + description: Use of rigid water in the simulation. + $comment: Use of rigid water in the simulation. Flexible water molecules usually + require a slower taken timestep by the used integrator. + type: boolean + iniseed: + default: 917 + title: Simulation seed. + description: Set a pseudo-random seed for the simulation. + $comment: Set a pseudo-random seed for the simulation. This defines how the + initial velocities are created, but has no effect on the randomicity of + the solvation box. + type: number + maximum: 1000000 + minimum: 0 + ion_concentration: + default: 0.15 + title: Ion concentration. + description: Ion concentration in Molar. + $comment: Ion concentration in Molar. + type: number + maximum: 5 + minimum: 0 + solv_equilibration: + default: true + title: Process the solvent equilibration phase. + description: Process the solvent equilibration phase. + $comment: Process the solvent equilibration phase. If 'true', the solvent + will be equilibrated while constraining proteins positions to intial ones. + type: boolean + required: [] + additionalProperties: false + uiSchema: + forcefield: + ui:group: force field + explicit_solvent_model: + ui:group: force field + keep_solvent: + ui:group: post processing + implicit_solvent: + ui:group: force field + implicit_solvent_model: + ui:group: force field + add_extra_particles_for_forcefield: + ui:group: force field + constraints: + ui:group: restraints + sampling_factor: + ui:group: sampling + temperature_kelvin: + ui:group: sampling + remove_center_of_mass_motion: + ui:group: sampling + generate_ensemble: + ui:group: post processing + rigid_water: + ui:group: restraints + iniseed: + ui:group: sampling + ion_concentration: + ui:group: sampling + solv_equilibration: + ui:group: sampling + tomlSchema: {} - id: rigidbody category: sampling label: Rigid-body docking sampling module diff --git a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml index 6dba33e..1379be0 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml @@ -6911,6 +6911,317 @@ nodes: tolerance: ui:group: module tomlSchema: {} +- id: openmm + category: refinement + label: OpenMM refinement module for HADDOCK3. + description: HADDOCK3 OpenMM module. + schema: + type: object + properties: + forcefield: + default: amber14-all.xml + title: Forcefield used by OpenMM. + description: Forcefields that can be used by OpenMM. + $comment: Forcefields that can be used by OpenMM. + type: string + minLength: 10 + maxLength: 100 + enum: + - amber14-all.xml + - amber14/protein.ff14SB.xml + - amber14/protein.ff15ipq.xml + - amber14/DNA.OL15.xml + - amber14/DNA.bsc1.xml + - amber14/RNA.OL3.xml + - amber14/lipid17.xml + - amber14/GLYCAM_06j-1.xml + - charmm36.xml + explicit_solvent_model: + default: amber14/tip3p.xml + title: Explicit solvent models. + description: Solvent models supported by the OpenMM modeller to build the + water solvation box. + $comment: Solvent models supported by the OpenMM modeller to build the water + solvation box. + type: string + minLength: 0 + maxLength: 100 + enum: + - amber14/tip3p.xml + - amber14/spce.xml + - charmm36/spce.xml + - amber14/tip4pew.xml + - charmm36/tip4pew.xml + - charmm36/tip5p.xml + ph: + default: 7.4 + title: pH of the buffer. + description: pH of the buffer. + $comment: pH of the buffer. This has an infulence on the protonation states + of the resiudes. + type: number + maximum: 12 + minimum: -3.0 + keep_solvent: + default: false + title: Whether-or-not solvent be removed from provided structures. + description: Whether-or-not solvent be removed from provided structures. + $comment: Whether-or-not solvent be removed from provided structures. If 'false', + all HETATM atoms will be removed. + type: boolean + implicit_solvent: + default: false + title: Indicate use of implicit solvent. + description: Indicate use of implicit solvent, avoids building a water solvation + box around pdbs. + $comment: Indicate use of implicit solvent, avoids building a water solvation + box around pdbs. + type: boolean + implicit_solvent_model: + default: implicit/hct.xml + title: Implicit solvent models. + description: Implicit solvent models supported by OpenMM. + $comment: Implicit solvent models supported by OpenMM. + type: string + minLength: 0 + maxLength: 100 + enum: + - implicit/hct.xml + - implicit/obc1.xml + - implicit/obc2.xml + - implicit/gbn.xml + - implicit/gbn2.xml + add_extra_particles_for_forcefield: + default: false + title: Add extra particles for forcefield. + description: Add extra particles for forcefield if needed such as e.g. Drude + particles. + $comment: Add extra particles for forcefield if needed such as e.g. Drude + particles. + type: boolean + timestep_ps: + default: 0.002 + title: Timestep definition. + description: Definition of timestep used by the integrator to progress the + simulation. + $comment: Definition of timestep used by the integrator to progress the simulation. + type: number + maximum: 0.004 + minimum: 0.001 + constraints: + default: HBonds + title: Integration constraints. + description: Integration constraints used to allow for larger integration + time step. + $comment: Integration constraints used to allow for larger integration time + step. For extra info see http://docs.openmm.org/latest/userguide/application/02_running_sims.html#constraints + type: string + minLength: 1 + maxLength: 20 + enum: + - None + - HBonds + - AllBonds + - HAngles + equilibration_timesteps: + default: 3000 + title: Equilibration timesteps. + description: Equilibration timesteps performed without saving the simulation + state. + $comment: Equilibration timesteps performed without saving the simulation + state. + type: number + maximum: 100000 + minimum: 0 + simulation_timesteps: + default: 2000 + title: Simulation timesteps. + description: Simulation timesteps performed during the simulation. + $comment: Simulation timesteps performed during the simulation. + type: number + maximum: 1000000 + minimum: 0 + sampling_factor: + default: 1 + title: Number of simulation replicas. + description: Number of simulation replicas. + $comment: Number of simulation replicas. + type: number + maximum: 20 + minimum: 1 + temperature_kelvin: + default: 298.15 + title: Average temperature. + description: Average temperature used by e.g. the integrator or by for temperature + coupling. + $comment: Average temperature used by e.g. the integrator or by for temperature + coupling. + type: number + maximum: 1000.0 + minimum: 1.0 + remove_center_of_mass_motion: + default: true + title: Remove center of mass motion. + description: Remove center of mass motion when overall molecular drift is + detected. + $comment: Remove center of mass motion when overall molecular drift is detected. + type: boolean + generate_ensemble: + default: true + title: Generate ensemble of configurations. + description: Generate ensemble of configurations. + $comment: If 'true', generates 1 single ensemble .pdb file holding various + configurations; composed of the equilibrated one, all intermediates and + the final one. If 'false', only return the last configuration obtained after + 'simulation_timesteps' steps. + type: boolean + save_intermediate: + default: 1 + title: Number of intermediate configurations to save. + description: Number of intermediate configurations to save during the simulation. + $comment: Number of intermediate configurations to save during the simulation. + The code divides the length of the simulation (simulation_timesteps) by + this parameter to get how often configurations should be saved. + type: number + maximum: 100 + minimum: 0 + padding: + default: 1.0 + title: Padding value in nanometers. + description: Padding value in nanometers. + $comment: Padding value in nanometers. This is used to create the solvation + box by adding water molecules around the molecule up to this padding distance. + When performing a long refinement of a complex, increase this parameter + as the molecules will likely move away from each other. + type: number + maximum: 10 + minimum: 0.3 + rigid_water: + default: true + title: Use rigid water. + description: Use of rigid water in the simulation. + $comment: Use of rigid water in the simulation. Flexible water molecules usually + require a slower taken timestep by the used integrator. + type: boolean + iniseed: + default: 917 + title: Simulation seed. + description: Set a pseudo-random seed for the simulation. + $comment: Set a pseudo-random seed for the simulation. This defines how the + initial velocities are created, but has no effect on the randomicity of + the solvation box. + type: number + maximum: 1000000 + minimum: 0 + ion_concentration: + default: 0.15 + title: Ion concentration. + description: Ion concentration in Molar. + $comment: Ion concentration in Molar. + type: number + maximum: 5 + minimum: 0 + solv_equilibration: + default: true + title: Process the solvent equilibration phase. + description: Process the solvent equilibration phase. + $comment: Process the solvent equilibration phase. If 'true', the solvent + will be equilibrated while constraining proteins positions to intial ones. + type: boolean + solv_eq_max_temperature_kelvin: + default: 310.0 + title: Upper boundary of temperature to reach during solvent eauilibration + phase. + description: Upper boundary of temperature to reach during solvent eauilibration + phase. + $comment: Upper boundary of temperature to reach during solvent eauilibration + phase. + type: number + maximum: 400 + minimum: 1 + solv_eq_stepsize_fs: + default: 2.0 + title: Step size for the solvent equilibration phase. + description: Step size (in femptoseconds) for the solvent equilibration phase. + $comment: Step size (in femptoseconds) for the solvent equilibration phase. + type: number + maximum: 4 + minimum: 0.5 + solv_eq_timesteps: + default: 500 + title: Number of timesteps to be performed during solvent equilibration phase. + description: Number of timesteps to be performed during solvent equilibration + phase. + $comment: Number of timesteps to be performed during solvent equilibration + phase. + type: number + maximum: 10000 + minimum: 10 + solv_eq_spring_constant: + default: 20.0 + title: Spring constant (k) used to restrain protein coordinates during solvent + equilibration phase. + description: Spring constant (k) used to restrain protein coordintes during + solvent equilibration phase. + $comment: Spring constant (k) used to restrain protein coordinates during + solvent equilibration phase. + type: number + maximum: 10000 + minimum: 0 + required: [] + additionalProperties: false + uiSchema: + forcefield: + ui:group: force field + explicit_solvent_model: + ui:group: force field + ph: + ui:group: simulation + keep_solvent: + ui:group: post processing + implicit_solvent: + ui:group: force field + implicit_solvent_model: + ui:group: force field + add_extra_particles_for_forcefield: + ui:group: force field + timestep_ps: + ui:group: sampling + constraints: + ui:group: restraints + equilibration_timesteps: + ui:group: sampling + simulation_timesteps: + ui:group: sampling + sampling_factor: + ui:group: sampling + temperature_kelvin: + ui:group: sampling + remove_center_of_mass_motion: + ui:group: sampling + generate_ensemble: + ui:group: post processing + save_intermediate: + ui:group: sampling + padding: + ui:group: sampling + rigid_water: + ui:group: restraints + iniseed: + ui:group: sampling + ion_concentration: + ui:group: sampling + solv_equilibration: + ui:group: sampling + solv_eq_max_temperature_kelvin: + ui:group: sampling + solv_eq_stepsize_fs: + ui:group: sampling + solv_eq_timesteps: + ui:group: sampling + solv_eq_spring_constant: + ui:group: sampling + tomlSchema: {} - id: rigidbody category: sampling label: Rigid-body docking sampling module diff --git a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml index 4c16ba5..d923a96 100644 --- a/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml +++ b/packages/haddock3_catalog/public/catalog/haddock3.guru.yaml @@ -7296,6 +7296,317 @@ nodes: log_level: ui:group: module tomlSchema: {} +- id: openmm + category: refinement + label: OpenMM refinement module for HADDOCK3. + description: HADDOCK3 OpenMM module. + schema: + type: object + properties: + forcefield: + default: amber14-all.xml + title: Forcefield used by OpenMM. + description: Forcefields that can be used by OpenMM. + $comment: Forcefields that can be used by OpenMM. + type: string + minLength: 10 + maxLength: 100 + enum: + - amber14-all.xml + - amber14/protein.ff14SB.xml + - amber14/protein.ff15ipq.xml + - amber14/DNA.OL15.xml + - amber14/DNA.bsc1.xml + - amber14/RNA.OL3.xml + - amber14/lipid17.xml + - amber14/GLYCAM_06j-1.xml + - charmm36.xml + explicit_solvent_model: + default: amber14/tip3p.xml + title: Explicit solvent models. + description: Solvent models supported by the OpenMM modeller to build the + water solvation box. + $comment: Solvent models supported by the OpenMM modeller to build the water + solvation box. + type: string + minLength: 0 + maxLength: 100 + enum: + - amber14/tip3p.xml + - amber14/spce.xml + - charmm36/spce.xml + - amber14/tip4pew.xml + - charmm36/tip4pew.xml + - charmm36/tip5p.xml + ph: + default: 7.4 + title: pH of the buffer. + description: pH of the buffer. + $comment: pH of the buffer. This has an infulence on the protonation states + of the resiudes. + type: number + maximum: 12 + minimum: -3.0 + keep_solvent: + default: false + title: Whether-or-not solvent be removed from provided structures. + description: Whether-or-not solvent be removed from provided structures. + $comment: Whether-or-not solvent be removed from provided structures. If 'false', + all HETATM atoms will be removed. + type: boolean + implicit_solvent: + default: false + title: Indicate use of implicit solvent. + description: Indicate use of implicit solvent, avoids building a water solvation + box around pdbs. + $comment: Indicate use of implicit solvent, avoids building a water solvation + box around pdbs. + type: boolean + implicit_solvent_model: + default: implicit/hct.xml + title: Implicit solvent models. + description: Implicit solvent models supported by OpenMM. + $comment: Implicit solvent models supported by OpenMM. + type: string + minLength: 0 + maxLength: 100 + enum: + - implicit/hct.xml + - implicit/obc1.xml + - implicit/obc2.xml + - implicit/gbn.xml + - implicit/gbn2.xml + add_extra_particles_for_forcefield: + default: false + title: Add extra particles for forcefield. + description: Add extra particles for forcefield if needed such as e.g. Drude + particles. + $comment: Add extra particles for forcefield if needed such as e.g. Drude + particles. + type: boolean + timestep_ps: + default: 0.002 + title: Timestep definition. + description: Definition of timestep used by the integrator to progress the + simulation. + $comment: Definition of timestep used by the integrator to progress the simulation. + type: number + maximum: 0.004 + minimum: 0.001 + constraints: + default: HBonds + title: Integration constraints. + description: Integration constraints used to allow for larger integration + time step. + $comment: Integration constraints used to allow for larger integration time + step. For extra info see http://docs.openmm.org/latest/userguide/application/02_running_sims.html#constraints + type: string + minLength: 1 + maxLength: 20 + enum: + - None + - HBonds + - AllBonds + - HAngles + equilibration_timesteps: + default: 3000 + title: Equilibration timesteps. + description: Equilibration timesteps performed without saving the simulation + state. + $comment: Equilibration timesteps performed without saving the simulation + state. + type: number + maximum: 100000 + minimum: 0 + simulation_timesteps: + default: 2000 + title: Simulation timesteps. + description: Simulation timesteps performed during the simulation. + $comment: Simulation timesteps performed during the simulation. + type: number + maximum: 1000000 + minimum: 0 + sampling_factor: + default: 1 + title: Number of simulation replicas. + description: Number of simulation replicas. + $comment: Number of simulation replicas. + type: number + maximum: 20 + minimum: 1 + temperature_kelvin: + default: 298.15 + title: Average temperature. + description: Average temperature used by e.g. the integrator or by for temperature + coupling. + $comment: Average temperature used by e.g. the integrator or by for temperature + coupling. + type: number + maximum: 1000.0 + minimum: 1.0 + remove_center_of_mass_motion: + default: true + title: Remove center of mass motion. + description: Remove center of mass motion when overall molecular drift is + detected. + $comment: Remove center of mass motion when overall molecular drift is detected. + type: boolean + generate_ensemble: + default: true + title: Generate ensemble of configurations. + description: Generate ensemble of configurations. + $comment: If 'true', generates 1 single ensemble .pdb file holding various + configurations; composed of the equilibrated one, all intermediates and + the final one. If 'false', only return the last configuration obtained after + 'simulation_timesteps' steps. + type: boolean + save_intermediate: + default: 1 + title: Number of intermediate configurations to save. + description: Number of intermediate configurations to save during the simulation. + $comment: Number of intermediate configurations to save during the simulation. + The code divides the length of the simulation (simulation_timesteps) by + this parameter to get how often configurations should be saved. + type: number + maximum: 100 + minimum: 0 + padding: + default: 1.0 + title: Padding value in nanometers. + description: Padding value in nanometers. + $comment: Padding value in nanometers. This is used to create the solvation + box by adding water molecules around the molecule up to this padding distance. + When performing a long refinement of a complex, increase this parameter + as the molecules will likely move away from each other. + type: number + maximum: 10 + minimum: 0.3 + rigid_water: + default: true + title: Use rigid water. + description: Use of rigid water in the simulation. + $comment: Use of rigid water in the simulation. Flexible water molecules usually + require a slower taken timestep by the used integrator. + type: boolean + iniseed: + default: 917 + title: Simulation seed. + description: Set a pseudo-random seed for the simulation. + $comment: Set a pseudo-random seed for the simulation. This defines how the + initial velocities are created, but has no effect on the randomicity of + the solvation box. + type: number + maximum: 1000000 + minimum: 0 + ion_concentration: + default: 0.15 + title: Ion concentration. + description: Ion concentration in Molar. + $comment: Ion concentration in Molar. + type: number + maximum: 5 + minimum: 0 + solv_equilibration: + default: true + title: Process the solvent equilibration phase. + description: Process the solvent equilibration phase. + $comment: Process the solvent equilibration phase. If 'true', the solvent + will be equilibrated while constraining proteins positions to intial ones. + type: boolean + solv_eq_max_temperature_kelvin: + default: 310.0 + title: Upper boundary of temperature to reach during solvent eauilibration + phase. + description: Upper boundary of temperature to reach during solvent eauilibration + phase. + $comment: Upper boundary of temperature to reach during solvent eauilibration + phase. + type: number + maximum: 400 + minimum: 1 + solv_eq_stepsize_fs: + default: 2.0 + title: Step size for the solvent equilibration phase. + description: Step size (in femptoseconds) for the solvent equilibration phase. + $comment: Step size (in femptoseconds) for the solvent equilibration phase. + type: number + maximum: 4 + minimum: 0.5 + solv_eq_timesteps: + default: 500 + title: Number of timesteps to be performed during solvent equilibration phase. + description: Number of timesteps to be performed during solvent equilibration + phase. + $comment: Number of timesteps to be performed during solvent equilibration + phase. + type: number + maximum: 10000 + minimum: 10 + solv_eq_spring_constant: + default: 20.0 + title: Spring constant (k) used to restrain protein coordinates during solvent + equilibration phase. + description: Spring constant (k) used to restrain protein coordintes during + solvent equilibration phase. + $comment: Spring constant (k) used to restrain protein coordinates during + solvent equilibration phase. + type: number + maximum: 10000 + minimum: 0 + required: [] + additionalProperties: false + uiSchema: + forcefield: + ui:group: force field + explicit_solvent_model: + ui:group: force field + ph: + ui:group: simulation + keep_solvent: + ui:group: post processing + implicit_solvent: + ui:group: force field + implicit_solvent_model: + ui:group: force field + add_extra_particles_for_forcefield: + ui:group: force field + timestep_ps: + ui:group: sampling + constraints: + ui:group: restraints + equilibration_timesteps: + ui:group: sampling + simulation_timesteps: + ui:group: sampling + sampling_factor: + ui:group: sampling + temperature_kelvin: + ui:group: sampling + remove_center_of_mass_motion: + ui:group: sampling + generate_ensemble: + ui:group: post processing + save_intermediate: + ui:group: sampling + padding: + ui:group: sampling + rigid_water: + ui:group: restraints + iniseed: + ui:group: sampling + ion_concentration: + ui:group: sampling + solv_equilibration: + ui:group: sampling + solv_eq_max_temperature_kelvin: + ui:group: sampling + solv_eq_stepsize_fs: + ui:group: sampling + solv_eq_timesteps: + ui:group: sampling + solv_eq_spring_constant: + ui:group: sampling + tomlSchema: {} - id: rigidbody category: sampling label: Rigid-body docking sampling module