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Andre Lanrezac
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feat(example): Add Maltoporin example
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‎example/IMPALA/Brasseur/Maltoporin/1AF6.pdb‎

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‎example/IMPALA/Brasseur/Maltoporin/1AF6_in_membrane.pdb‎

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‎example/IMPALA/Brasseur/Maltoporin/all_atoms/Makefile‎

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BASE_MK := $(shell echo $(PWD) | sed -E 's|(.*example).*|\1/base.mk|')
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# Inclure base.mk si trouvé
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ifneq ($(wildcard $(BASE_MK)),)
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include $(BASE_MK)
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# $(info Included: $(BASE_MK))
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endif
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# RAW PDB INPUT
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RAW_PDB = ../1AF6_in_membrane.pdb
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# PDB2SPN INPUTS
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FF = $(BS_DATA_DIR)/forcefield/amber.ff
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GRP = $(BS_DATA_DIR)/reducerules/amber.grp
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CUTOFF = 5.0
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STIFFNESS = 30.0
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# Prepare the input files for the simulation
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prep : pdb2spn
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# ------------------------------------------------------------------------------
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# Usage: run the command make usage
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# ------------------------------------------------------------------------------

‎example/IMPALA/Brasseur/Maltoporin/all_atoms/UMolState.py‎

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# Changes in the "BioSpring" branch of UnityMolX:
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# - LoadNCFromPath is a new function
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# - The UMol working directory is set to the directory of this history file (PythonConsole2.cs > ExecuteScript)
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LoadNCFromPath(filePath="model.nc")
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clearSelections()
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setStructurePositionRotation("model", Vector3(0.0000, 0.0000, 0.0000), Vector3(0.0000, 0.0000, 0.0000))
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#Save parent position
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setMolParentTransform( Vector3(0.1525, -0.0934, 0.1519), Vector3(0.0145, 0.0145, 0.0145), Vector3(282.9991, 180.0000, 206.8996), Vector3(0.1350, -0.1200, 0.1528) )
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ShowMeshMembrane()
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UpdateMeshMembraneSize(100)

‎example/IMPALA/Brasseur/Maltoporin/all_atoms/param.msp‎

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#--- GeneralSimulation ---
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simulation.timestep = 1
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simulation.samplerate = 100
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#simulation.nbsteps = 10000
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#--- GeneralSimulation:Trajectory ---
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csvsampling.enable = 0
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csvsampling.path = csv_results/ims_out.csv
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csvsampling.frequency = 10000
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#--- SpringNetwork ---
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spring.enable = 0
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viscosity.enable = 1
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viscosity.value = 0.001
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#--- FF:IMPALA ---
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impala.enable = 1
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impala.scale = 1.0
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#--- InsertionVector ---
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insertionvector.enable = 1
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# THR-40-CA GLN-48-CA, check PDB file & biospring output to verify
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insertionvector.vector = 298 360
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#--- Rigid body ---
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rigidbody.enable = 1
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rigidbody.enablesampling = 0
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rigidbody.enablemontecarlo = 0
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rigidbody.montecarlo_translation_norm = 0.01
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rigidbody.montecarlo_rotation_norm = 0.01
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rigidbody.montecarlo_temperature = 298.1

‎example/IMPALA/Brasseur/Maltoporin/lewitt/Makefile‎

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BASE_MK := $(shell echo $(PWD) | sed -E 's|(.*example).*|\1/base.mk|')
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# Inclure base.mk si trouvé
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ifneq ($(wildcard $(BASE_MK)),)
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include $(BASE_MK)
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# $(info Included: $(BASE_MK))
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endif
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# RAW PDB INPUT
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RAW_PDB = ../1AF6_in_membrane.pdb
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# PDB2SPN INPUTS
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FF = $(BS_DATA_DIR)/forcefield/CAallresBaaden.ff
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GRP = $(BS_DATA_DIR)/reducerules/CAallresBaaden.grp
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CUTOFF = 9.0
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STIFFNESS = 30.0
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# Prepare the input files for the simulation
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prep : pdb2spn
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# ------------------------------------------------------------------------------
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# Usage: run the command make usage
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# ------------------------------------------------------------------------------

‎example/IMPALA/Brasseur/Maltoporin/lewitt/UMolState.py‎

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# Changes in the "BioSpring" branch of UnityMolX:
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# - LoadNCFromPath is a new function
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# - The UMol working directory is set to the directory of this history file (PythonConsole2.cs > ExecuteScript)
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LoadNCFromPath(filePath="model.nc")
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clearSelections()
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setStructurePositionRotation("model", Vector3(0.0000, 0.0000, 0.0000), Vector3(0.0000, 0.0000, 0.0000))
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#Save parent position
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setMolParentTransform( Vector3(0.1525, -0.0934, 0.1519), Vector3(0.0145, 0.0145, 0.0145), Vector3(282.9991, 180.0000, 206.8996), Vector3(0.1350, -0.1200, 0.1528) )
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ShowMeshMembrane()
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UpdateMeshMembraneSize(100)

‎example/IMPALA/Brasseur/Maltoporin/lewitt/param.msp‎

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#--- GeneralSimulation ---
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simulation.timestep = 1
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simulation.samplerate = 100
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#simulation.nbsteps = 10000
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#--- GeneralSimulation:Trajectory ---
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csvsampling.enable = 0
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csvsampling.path = csv_results/ims_out.csv
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csvsampling.frequency = 10000
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#--- SpringNetwork ---
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spring.enable = 0
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viscosity.enable = 1
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viscosity.value = 0.001
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#--- FF:IMPALA ---
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impala.enable = 1
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impala.scale = 1.0
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#--- InsertionVector ---
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insertionvector.enable = 1
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# THR-40-CA GLN-48-CA, check PDB file & biospring output to verify
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insertionvector.vector = 298 360
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#--- Rigid body ---
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rigidbody.enable = 1
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rigidbody.enablesampling = 0
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rigidbody.enablemontecarlo = 0
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rigidbody.montecarlo_translation_norm = 0.01
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rigidbody.montecarlo_rotation_norm = 0.01
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rigidbody.montecarlo_temperature = 298.1

‎example/IMPALA/Brasseur/Maltoporin/martini3/Makefile‎

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BASE_MK := $(shell echo $(PWD) | sed -E 's|(.*example).*|\1/base.mk|')
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# Inclure base.mk si trouvé
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ifneq ($(wildcard $(BASE_MK)),)
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include $(BASE_MK)
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# $(info Included: $(BASE_MK))
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endif
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# RAW PDB INPUT
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RAW_PDB = ../1AF6_in_membrane.pdb
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# PDB2SPN INPUTS
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FF = $(BS_DATA_DIR)/martini/forcefield/martini_octanol.ff
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GRP = $(BS_DATA_DIR)/martini/reducerules/martini.grp
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CUTOFF = 5.0
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STIFFNESS = 30.0
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# Prepare the input files for the simulation
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prep : martinize pause pdb2spn
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# ------------------------------------------------------------------------------
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# Usage: run the command make usage
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# ------------------------------------------------------------------------------

‎example/IMPALA/Brasseur/Maltoporin/martini3/UMolState.py‎

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# Changes in the "BioSpring" branch of UnityMolX:
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# - LoadNCFromPath is a new function
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# - The UMol working directory is set to the directory of this history file (PythonConsole2.cs > ExecuteScript)
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LoadNCFromPath(filePath="model.nc")
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clearSelections()
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setStructurePositionRotation("model", Vector3(0.0000, 0.0000, 0.0000), Vector3(0.0000, 0.0000, 0.0000))
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#Save parent position
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setMolParentTransform( Vector3(0.1525, -0.0934, 0.1519), Vector3(0.0145, 0.0145, 0.0145), Vector3(282.9991, 180.0000, 206.8996), Vector3(0.1350, -0.1200, 0.1528) )
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ShowMeshMembrane()
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UpdateMeshMembraneSize(100)

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