diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1A3N.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1A3N.txt deleted file mode 100644 index f1539408..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1A3N.txt +++ /dev/null @@ -1,127 +0,0 @@ -Query from the user: Simulate 1A3N in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating a protein, 1A3N, in water at a specific temperature (280K). Before running the simulation, the protein structure needs to be cleaned. The steps will include cleaning the protein using the CleaningToolFunction, setting up the simulation environment with water using SetUpandRunFunction, and adjusting the temperature to 280K. I will start by cleaning the protein. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1A3N", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```Thought: The previous attempt to clean the protein failed because the file was not found. This could mean that the PDB ID was incorrect or not available in the current path registry. I will use the PDBFileDownloader tool to download the PDB file for the protein 1A3N and then attempt to clean it again using the CleaningToolFunction. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1A3N" - } -} -```PDB file found with this ID: 1A3N -Now that the PDB file for the protein 1A3N has been successfully downloaded, I will proceed to clean the protein using the CleaningToolFunction with the downloaded PDB ID. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1A3N_132127", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein 1A3N has been successfully cleaned and is now ready for simulation. The next step is to set up and run the molecular dynamics simulation in water at the specified temperature of 280K. I will use the SetUpandRunFunction tool to perform this task, ensuring that the system is solvated with water and the temperature is set to 280K. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1A3N_132141", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup failed because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME. I will correct this by adding the `ewaldErrorTolerance` parameter to the system parameters and then reattempt the simulation setup using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1A3N_132141", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1A3N_132141_20240213_132217.py -['restartscript.sh', 'LICENSE', '.pytest_cache', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'TRAJ_sim_132217_1A3N_132141_20240213_132219.dcd', 'README.md', '.secrets.baseline', 'setup.py', '.mypy_cache', '.gitignore', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'LOG_sim_132217_1A3N_132141_20240213_132219.txt', 'environment.yaml', '.env.example', '.git', '.vscode', 'notebooks'] -Final Answer: The molecular dynamics simulation of the protein 1A3N in water at 280K has been successfully completed after cleaning the protein and setting up the simulation with the correct parameters. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1ATN.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1ATN.txt deleted file mode 100644 index 7ffb0aa0..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1ATN.txt +++ /dev/null @@ -1,112 +0,0 @@ -Query from the user: Simulate 1ATN in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating the protein with PDB ID 1ATN in water at a temperature of 280K. Before running the simulation, the protein structure needs to be cleaned. The first step is to download the PDB file for 1ATN and then clean it using the CleaningToolFunction. After cleaning, I will set up and run the simulation using the SetUpandRunFunction, ensuring that the temperature is set to 280K and the system is solvated with water. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1ATN" - } -} -``` -PDB file found with this ID: 1ATN -Now that the PDB file for 1ATN has been successfully downloaded, the next step is to clean the protein structure using the CleaningToolFunction. This will involve removing heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and removing water. After cleaning, the protein will be ready for simulation. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1ATN_135555", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein with PDB ID 1ATN has been cleaned successfully and is now ready for simulation. The next step is to set up and run the simulation using the SetUpandRunFunction. I will ensure that the temperature is set to 280K, the system is solvated with water, and the appropriate forcefield is selected for the simulation. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1ATN_135616", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup encountered an error because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME (Particle Mesh Ewald). I need to add this parameter to the system parameters and re-run the SetUpandRunFunction to initiate the simulation correctly. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1ATN_135616", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1ATN_135616_20240213_135658.py -['restartscript.sh', 'Attempt_1_1TUP.txt', 'LICENSE', '.pytest_cache', 'dev-requirements.txt', '.pre-commit-config.yaml', 'TRAJ_sim_135658_1ATN_135616_20240213_135704.dcd', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'LOG_sim_135658_1ATN_135616_20240213_135704.txt', 'Attempt_1_1A3N.txt', 'setup.py', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'Attempt_1_1BR1.txt', 'notebooks'] -Final Answer: The simulation of the protein with PDB ID 1ATN in water at 280K has been successfully completed after cleaning the protein structure and setting the correct simulation parameters, including the `ewaldErrorTolerance` for the PME nonbonded method. The simulation ran with the specified forcefield files, system parameters, integrator parameters, and simulation parameters. The results are saved and can be analyzed to understand the behavior of the protein at the given temperature and conditions. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1BO9.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1BO9.txt deleted file mode 100644 index 8b169303..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1BO9.txt +++ /dev/null @@ -1,101 +0,0 @@ -Query from the user: Simulate 1BO9 in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating a protein (1BO9) in water at a specific temperature (280K). Before running the simulation, the protein structure needs to be cleaned. The first step is to download the protein structure file using its PDB ID. Then, I will clean the protein using the CleaningToolFunction. After that, I will set up and run the simulation with the specified temperature and in the presence of water using the SetUpandRunFunction. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1BO9" - } -} -``` - -PDB file found with this ID: 1BO9 -The PDB file for the protein 1BO9 has been successfully downloaded. The next step is to clean the protein structure using the CleaningToolFunction. This will involve removing any heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and removing water molecules that may be present in the crystal structure. After cleaning, the protein will be ready for simulation. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1BO9_143249", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein structure has been cleaned successfully, and I now have the cleaned PDB file. The next step is to set up and run the molecular dynamics simulation of the cleaned protein in water at the specified temperature of 280K. I will use the SetUpandRunFunction tool to perform this task. I will need to specify the system parameters to include solvation and set the temperature to 280K in the integrator parameters. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1BO9_143306", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup failed because the `ewaldErrorTolerance` parameter was not specified, which is required when using the Particle Mesh Ewald (PME) method for handling long-range electrostatic interactions. I need to include this parameter in the system settings and retry the simulation setup. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1BO9_143306", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Cannot neutralize the system because the charge is greater than the number of available positions for ions diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1BR1.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1BR1.txt deleted file mode 100644 index b78de4ba..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1BR1.txt +++ /dev/null @@ -1,137 +0,0 @@ -Query from the user: Simulate 1BR1 in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating the protein with PDB ID 1BR1 in water at a temperature of 280K. Before running the simulation, the protein structure must be cleaned to ensure it is suitable for simulation. This involves removing any heterogens, adding missing atoms and hydrogens, and possibly replacing nonstandard residues. After cleaning, I will need to set up and run the simulation using the appropriate tools. The first step is to clean the protein using the CleaningToolFunction. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1BR1", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The previous attempt to clean the protein with PDB ID 1BR1 failed because the file was not found. It's possible that the PDB ID was incorrect or the file needs to be downloaded first. I will use the PDBFileDownloader tool to download the PDB file for 1BR1 before attempting to clean it again. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1BR1" - } -} -```PDB file found with this ID: 1BR1 -Now that the PDB file for 1BR1 has been successfully downloaded, I can proceed with cleaning the protein using the CleaningToolFunction. This step is essential to prepare the protein for simulation by removing any unwanted molecules, adding missing atoms and hydrogens, and replacing nonstandard residues if necessary. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1BR1_133702", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein with PDB ID 1BR1 has been successfully cleaned and is now ready for simulation. The next step is to set up and run the molecular dynamics simulation in water at the specified temperature of 280K. I will use the SetUpandRunFunction tool to perform this task, ensuring to specify the temperature and solvation parameters correctly. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1BR1_133804", - "forcefield_files": [], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1.0 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": [ - "step", - "potentialEnergy", - "temperature" - ] - } - } -} -```Setting default forcefields v2 -error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup failed because the `ewaldErrorTolerance` parameter was not specified, which is required when using the PME (Particle Mesh Ewald) method for the nonbonded interactions. I will correct this by adding the `ewaldErrorTolerance` parameter to the system parameters and then reattempt the simulation setup using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1BR1_133804", - "forcefield_files": [], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1.0 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": [ - "step", - "potentialEnergy", - "temperature" - ] - } - } -} -```Setting default forcefields v2 -Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1BR1_133804_20240213_133850.py -['restartscript.sh', 'Attempt_1_1TUP.txt', 'LICENSE', '.pytest_cache', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'TRAJ_sim_133850_1BR1_133804_20240213_133905.dcd', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'setup.py', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'LOG_sim_133850_1BR1_133804_20240213_133905.txt', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'notebooks'] -Final Answer: The molecular dynamics simulation of the protein with PDB ID 1BR1 in water at 280K has been successfully completed after cleaning the protein structure. The simulation was set up with the PME method for nonbonded interactions, constraints on hydrogen bonds, and a Langevin integrator to maintain the temperature at 280K. The simulation ran for 5000 steps, and parameters such as potential energy and temperature were recorded at regular intervals. The simulation data can be used for further analysis to understand the behavior of the protein under the specified conditions. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1IGT.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1IGT.txt deleted file mode 100644 index 8bec8da6..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1IGT.txt +++ /dev/null @@ -1,127 +0,0 @@ -Query from the user: Simulate 1IGT in water at 280K. Dont forget to clean the protein first - -Thought: To simulate the protein 1IGT in water at 280K, I need to first clean the protein using the CleaningToolFunction to prepare it for simulation. After cleaning, I will set up and run the simulation using the SetUpandRunFunction, ensuring that the system is solvated in water and the temperature is set to 280K. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1IGT", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```Thought: The previous attempt to clean the protein 1IGT failed because the file was not found. I need to download the PDB file for 1IGT before I can clean it. I will use the PDBFileDownloader tool to obtain the PDB file for 1IGT. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1IGT" - } -} -```PDB file found with this ID: 1IGT -Now that I have successfully downloaded the PDB file for 1IGT, I can proceed to clean the protein using the CleaningToolFunction. This step is necessary to prepare the protein for simulation by removing any unwanted molecules, adding missing atoms, and standardizing residues. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1IGT_141237", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```With the protein 1IGT now cleaned, the next step is to set up and run the molecular dynamics simulation. The simulation should be performed in water at a temperature of 280K. I will use the SetUpandRunFunction tool to perform this task, ensuring to specify the system parameters for solvation and the integrator parameters for the desired temperature. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1IGT_141251", - "forcefield_files": ["amber14-all.xml", "amber14/tip3p.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The previous attempt to run the simulation failed because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME. I will correct this by adding the `ewaldErrorTolerance` parameter to the system parameters and then reattempt the simulation setup and run using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1IGT_141251", - "forcefield_files": ["amber14-all.xml", "amber14/tip3p.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1IGT_141251_20240213_141348.py -['restartscript.sh', 'Attempt_1_1TUP.txt', 'Attempt_1_2RH1.txt', 'LICENSE', '.pytest_cache', 'Attempt_1_1ATN.txt', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'TRAJ_sim_141348_1IGT_141251_20240213_141352.dcd', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'LOG_sim_141348_1IGT_141251_20240213_141352.txt', 'setup.py', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'Attempt_1_1BR1.txt', 'notebooks'] -Final Answer: The molecular dynamics simulation of the protein 1IGT in water at 280K has been successfully completed after cleaning the protein and setting up the simulation with the correct parameters. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1PQ2.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1PQ2.txt deleted file mode 100644 index b0c6d4b3..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1PQ2.txt +++ /dev/null @@ -1,127 +0,0 @@ -Query from the user: Simulate 1PQ2 in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating the protein with PDB ID 1PQ2 in water at a temperature of 280K. Before running the simulation, I need to clean the protein structure to ensure it is suitable for molecular dynamics simulations. This typically involves removing any heteroatoms, adding missing atoms, and possibly adding hydrogens. Once the protein is cleaned, I can proceed to set up and run the simulation in a water environment at the specified temperature. I will use the CleaningToolFunction to clean the protein and then the SetUpandRunFunction to simulate the protein in water at 280K. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1PQ2", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```Thought: The previous attempt to clean the protein with PDB ID 1PQ2 failed because the file was not found. I need to download the PDB file for the protein before I can clean it. I will use the PDBFileDownloader tool to download the PDB file for 1PQ2. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1PQ2" - } -} -```PDB file found with this ID: 1PQ2 -Now that the PDB file for 1PQ2 has been successfully downloaded, I can proceed with cleaning the protein using the CleaningToolFunction. This step is essential to prepare the protein for simulation by removing any unwanted molecules, adding missing atoms, and standardizing the structure. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1PQ2_141837", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein with PDB ID 1PQ2 has been successfully cleaned and is now ready for simulation. The next step is to set up and run the molecular dynamics simulation in a water environment at the specified temperature of 280K. I will use the SetUpandRunFunction tool to perform this task, ensuring to specify the temperature and the inclusion of a water environment in the simulation parameters. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1PQ2_141851", - "forcefield_files": ["amber14-all.xml", "amber14/tip3p.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup failed because the ewaldErrorTolerance parameter was not specified, which is required when using the PME (Particle Mesh Ewald) method for handling long-range electrostatic interactions. I will correct this by adding the ewaldErrorTolerance parameter to the system_params and then reattempt the simulation setup using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1PQ2_141851", - "forcefield_files": ["amber14-all.xml", "amber14/tip3p.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1PQ2_141851_20240213_141930.py -['restartscript.sh', 'Attempt_1_1TUP.txt', 'Attempt_1_2RH1.txt', 'LICENSE', '.pytest_cache', 'Attempt_1_1ATN.txt', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'Attempt_1_1IGT.txt', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'TRAJ_sim_141930_1PQ2_141851_20240213_141939.dcd', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'setup.py', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', 'LOG_sim_141930_1PQ2_141851_20240213_141939.txt', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'Attempt_1_1BR1.txt', 'notebooks'] -Final Answer: The molecular dynamics simulation of the protein with PDB ID 1PQ2 in water at 280K has been successfully completed after cleaning the protein structure and setting up the simulation with the correct parameters, including the ewaldErrorTolerance for the PME method. The simulation ran for 5000 steps, recording the potential energy and temperature at every 50 steps. The results of this simulation can be used for further analysis to understand the behavior of the protein under the specified conditions. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1TRZ.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1TRZ.txt deleted file mode 100644 index 3f0ecf93..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1TRZ.txt +++ /dev/null @@ -1,113 +0,0 @@ -Query from the user: Simulate 1TRZ in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating a protein, 1TRZ, in water at 280K. Before running the simulation, the protein structure needs to be cleaned. The first step is to download the PDB file for 1TRZ using the PDBFileDownloader tool. After obtaining the file, I will use the CleaningToolFunction to clean the protein. Once the protein is cleaned, I will set up and run the simulation using the SetUpandRunFunction tool, ensuring that the temperature is set to 280K and the system is solvated with water. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1TRZ" - } -} -```PDB file found with this ID: 1TRZ -Now that the PDB file for 1TRZ has been successfully downloaded, the next step is to clean the protein structure. This involves removing any heterogens, adding missing atoms and hydrogens, replacing nonstandard residues, and removing water molecules that may be present in the crystal structure. I will use the CleaningToolFunction to perform these tasks. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1TRZ_132453", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein 1TRZ has been cleaned successfully, and I now have the cleaned PDB file. The next step is to set up and run the molecular dynamics simulation. I will use the SetUpandRunFunction tool to perform the simulation. I need to ensure that the temperature is set to 280K, the system is solvated with water, and the appropriate forcefield is applied. I will also make sure to set the system parameters to include a water model suitable for the simulation. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1TRZ_132505", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup encountered an error because the `ewaldErrorTolerance` parameter was not specified, which is required when the `nonbondedMethod` is set to PME (Particle Mesh Ewald). I will correct this by adding the `ewaldErrorTolerance` parameter to the system parameters and then reattempt the simulation setup using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1TRZ_132505", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1TRZ_132505_20240213_132542.py -['restartscript.sh', 'LICENSE', 'TRAJ_sim_132542_1TRZ_132505_20240213_132543.dcd', '.pytest_cache', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'setup.py', '.mypy_cache', '.gitignore', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'notebooks', 'LOG_sim_132542_1TRZ_132505_20240213_132543.txt'] -The molecular dynamics simulation of the protein 1TRZ in water at 280K has been successfully completed after cleaning the protein and setting the correct simulation parameters, including the ewaldErrorTolerance for the PME nonbonded method. The simulation ran for 5000 steps with recording intervals of 50 steps, capturing data on the step number, potential energy, and temperature throughout the simulation. - -Final Answer: The simulation of protein 1TRZ in water at 280K has been successfully completed. The cleaned protein structure was used, and the simulation parameters were set to include a Particle Mesh Ewald nonbonded method with an ewaldErrorTolerance of 0.0005, hydrogen bonds constraints, rigid water model, and Langevin integrator with a temperature of 280K. The simulation ran for 5000 steps, and data was recorded at 50-step intervals. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_1TUP.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_1TUP.txt deleted file mode 100644 index 4323e91d..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_1TUP.txt +++ /dev/null @@ -1,161 +0,0 @@ -Query from the user: Simulate 1TUP in water at 280K. Dont forget to clean the protein first - -Thought: The task involves simulating the protein with PDB ID 1TUP in water at 280K. Before running the simulation, the protein structure needs to be cleaned. The first step is to download the PDB file for 1TUP and then clean it using the CleaningToolFunction. After cleaning, I will set up and run the simulation using the SetUpandRunFunction, ensuring the temperature is set to 280K and the system is solvated in water. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1TUP", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The previous attempt to clean the protein with PDB ID 1TUP failed because the file was not found. It's possible that the PDB file for 1TUP is not present in the current file path registry. The first step should be to download the PDB file for 1TUP using the PDBFileDownloader tool. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "1TUP" - } -} -```PDB file found with this ID: 1TUP -Now that the PDB file for 1TUP has been successfully downloaded, the next step is to clean the protein using the CleaningToolFunction. This will prepare the protein for simulation by removing heterogens, adding missing atoms and hydrogens, and replacing nonstandard residues. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "1TUP_132803", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein with PDB ID 1TUP has been successfully cleaned and is now ready for simulation. The next step is to set up and run the molecular dynamics simulation using the SetUpandRunFunction tool. I will ensure that the temperature is set to 280K, the system is solvated in water, and the appropriate forcefield files are used. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1TUP_132828", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: constraintTolerance must be specified if rigidWater is True - Correct this and try again. - Everthing else is fine -The simulation setup failed because the constraintTolerance parameter was not specified, which is required when rigidWater is set to True. I will correct this by adding the constraintTolerance parameter to the system_params and then reattempt the simulation setup using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1TUP_132828", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup failed again because the ewaldErrorTolerance parameter was not specified, which is required when the nonbondedMethod is set to PME. I will correct this by adding the ewaldErrorTolerance parameter to the system_params and then reattempt the simulation setup using the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "1TUP_132828", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_1TUP_132828_20240213_132948.py -['restartscript.sh', 'LICENSE', '.pytest_cache', 'LOG_sim_132948_1TUP_132828_20240213_132954.txt', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'setup.py', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'notebooks', 'TRAJ_sim_132948_1TUP_132828_20240213_132954.dcd'] -Final Answer: The molecular dynamics simulation of the protein with PDB ID 1TUP in water at 280K has been successfully completed after cleaning the protein and setting up the simulation with the correct parameters. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_2RH1.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_2RH1.txt deleted file mode 100644 index 15c4c6f5..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_2RH1.txt +++ /dev/null @@ -1,128 +0,0 @@ -Query from the user: Simulate 2RH1 in water at 280K. Dont forget to clean the protein first - -Thought: The task requires simulating the protein with PDB ID 2RH1 in water at 280K. Before running the simulation, the protein structure must be cleaned to ensure it is suitable for molecular dynamics simulations. The first step is to download and clean the protein structure. Then, I will set up and run the simulation with the specified temperature and in a water environment. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "2RH1", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -``` -The previous attempt to clean the protein with PDB ID 2RH1 failed because the file was not found. It's possible that the PDB file needs to be downloaded first before it can be cleaned. I will download the PDB file for 2RH1 and then proceed with the cleaning process. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "2RH1" - } -} -```PDB file found with this ID: 2RH1 -Now that the PDB file for 2RH1 has been successfully downloaded, the next step is to clean the protein structure using the CleaningToolFunction. This will prepare the protein for simulation by replacing nonstandard residues, adding missing atoms, removing heterogens and water, and adding hydrogens at pH 7.0. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "2RH1_140550", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```The protein with PDB ID 2RH1 has been successfully cleaned and is now ready for simulation. The next step is to set up and run the molecular dynamics simulation in water at the specified temperature of 280K. I will use the SetUpandRunFunction tool to perform this task, ensuring that the system is solvated and the temperature is set to 280K. - -Action: -```json -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "2RH1_140559", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup failed because the ewaldErrorTolerance parameter was not specified, which is required when using the PME nonbonded method. I will correct this by adding the ewaldErrorTolerance parameter and then reattempt the simulation setup. - -Action: -```json -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "2RH1_140559", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_2RH1_140559_20240213_140650.py -['restartscript.sh', 'Attempt_1_1TUP.txt', 'LICENSE', '.pytest_cache', 'Attempt_1_1ATN.txt', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'TRAJ_sim_140650_2RH1_140559_20240213_140655.dcd', 'output_prompt_0.txt', 'st_app.py', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'setup.py', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'LOG_sim_140650_2RH1_140559_20240213_140655.txt', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'Attempt_1_1BR1.txt', 'notebooks'] -Final Answer: The molecular dynamics simulation of the protein with PDB ID 2RH1 in water at 280K has been successfully completed. The protein was first cleaned to prepare it for simulation, and then the simulation was set up and run with the specified parameters. The simulation used the Langevin integrator with a temperature of 280K, and the system was solvated in water using the PME method for handling long-range electrostatics. The simulation ran for 5000 steps, and data such as potential energy and temperature were recorded at intervals of 50 steps. The results of the simulation are now available for analysis. diff --git a/notebooks/rdf/testing_files/Test1/Attempt_1_2TNF.txt b/notebooks/rdf/testing_files/Test1/Attempt_1_2TNF.txt deleted file mode 100644 index f9055713..00000000 --- a/notebooks/rdf/testing_files/Test1/Attempt_1_2TNF.txt +++ /dev/null @@ -1,127 +0,0 @@ -Query from the user: Simulate 2TNF in water at 280K. Dont forget to clean the protein first - -Thought: The task involves multiple steps: first, I need to clean the protein 2TNF, then set up and run a molecular dynamics simulation of it in water at 280K. I will start by cleaning the protein using the CleaningToolFunction. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "2TNF", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```Thought: The file for the protein 2TNF was not found, which suggests that it may not be available in the current path registry or the ID might be incorrect. I will use the PDBFileDownloader tool to download the PDB file for the protein 2TNF. - -Action: -``` -{ - "action": "PDBFileDownloader", - "action_input": { - "query": "2TNF" - } -} -```PDB file found with this ID: 2TNF -Now that I have successfully downloaded the PDB file for 2TNF, I will proceed to clean the protein using the CleaningToolFunction, specifying the downloaded PDB file ID. - -Action: -``` -{ - "action": "CleaningToolFunction", - "action_input": { - "pdb_id": "2TNF_143023", - "replace_nonstandard_residues": true, - "add_missing_atoms": true, - "remove_heterogens": true, - "remove_water": true, - "add_hydrogens": true, - "add_hydrogens_ph": 7.0 - } -} -```With the protein 2TNF now cleaned, the next step is to set up and run a molecular dynamics simulation in water at 280K. I will use the SetUpandRunFunction tool to perform this task, ensuring to specify the temperature and solvation parameters. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "2TNF_143036", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```error found: ewaldErrorTolerance must be specified when - nonbondedMethod is PME - - Correct this and try again. - Everthing else is fine -The simulation setup requires an `ewaldErrorTolerance` value when using the PME method for nonbonded interactions. I will add this parameter to the system parameters and re-run the SetUpandRunFunction tool. - -Action: -``` -{ - "action": "SetUpandRunFunction", - "action_input": { - "pdb_id": "2TNF_143036", - "forcefield_files": ["amber14-all.xml", "amber14/tip3pfb.xml"], - "save": true, - "system_params": { - "nonbondedMethod": "PME", - "nonbondedCutoff": "1 * nanometers", - "ewaldErrorTolerance": 0.0005, - "constraints": "HBonds", - "rigidWater": true, - "constraintTolerance": 0.00001, - "solvate": true - }, - "integrator_params": { - "integrator_type": "LangevinMiddle", - "Temperature": "280 * kelvin", - "Friction": "1.0 / picoseconds", - "Timestep": "0.002 * picoseconds" - }, - "simmulation_params": { - "Ensemble": "NVT", - "Number of Steps": 5000, - "record_interval_steps": 50, - "record_params": ["step", "potentialEnergy", "temperature"] - } - } -} -```Building system... -Setting up integrator... -Creating simulation... -simulation set! -Performing energy minimization... -Minimization complete! -Equilibrating... -Simulating... -Done! -Standalone simulation script written to files/simulations/NVT_2TNF_143036_20240213_143106.py -['restartscript.sh', 'Attempt_1_1TUP.txt', 'Attempt_1_2RH1.txt', 'LICENSE', '.pytest_cache', 'Attempt_1_1ATN.txt', 'dev-requirements.txt', '.pre-commit-config.yaml', 'output_prompt_2.txt', 'output_prompt_3.txt', 'testingnotebook.ipynb', '.ruff_cache', 'ckpt', 'output_prompt_1.txt', 'output_prompt_0.txt', 'st_app.py', 'LOG_sim_143106_2TNF_143036_20240213_143107.txt', 'Attempt_1_1IGT.txt', 'tests', 'output_prompt_4.txt', 'output_prompt_5.txt', 'mdagent', 'README.md', '.secrets.baseline', 'Attempt_1_1A3N.txt', 'setup.py', 'Attempt_1_1PQ2.txt', 'Attempt_1_1TRZ.txt', '.mypy_cache', '.gitignore', 'TRAJ_sim_143106_2TNF_143036_20240213_143107.dcd', 'paths_registry.json', '.env', 'CONTRIBUTING.md', 'md_agent.egg-info', '.github', 'files', 'environment.yaml', '.env.example', '.git', '.vscode', 'Attempt_1_1BR1.txt', 'notebooks'] -Final Answer: The molecular dynamics simulation of the protein 2TNF in water at 280K has been successfully completed.