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Jgmedina95 committed Jul 11, 2024
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{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"import datetime\n",
"import os\n",
"from mdagent import MDAgent\n",
"import matplotlib.pyplot as plt"
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"date and time: 2024-07-10\n",
"time: 23:04:46\n",
"LLM: gpt-4o-2024-05-13 \n",
"Temperature: 0.1\n"
]
}
],
"source": [
"prompt24 = \"Analyze the rdf of the simulation of 1A3N solvated in water\"\n",
"llm_var = \"gpt-4o-2024-05-13\"\n",
"tools = \"all\"\n",
"agent = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools)\n",
"now = datetime.datetime.now()\n",
"date = now.strftime(\"%Y-%m-%d\")\n",
"print(\"date and time:\",date)\n",
"time = now.strftime(\"%H:%M:%S\")\n",
"print(\"time:\",time)\n",
"print(\"LLM: \",agent.llm.model_name,\"\\nTemperature: \",agent.llm.temperature)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Thought: To analyze the radial distribution function (RDF) of the simulation of the protein 1A3N solvated in water, I need to ensure that I have the necessary trajectory and topology files. I will use the RDFTool to perform this analysis.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"RDFTool\",\n",
" \"action_input\": {\n",
" \"input\": {\n",
" \"pdb_id\": \"1A3N\"\n",
" }\n",
" }\n",
"}\n",
"```Error in Inputs in RDF tool: Incorrect Inputs: Trajectory file ID ('trajectory_fileid')is required\n",
"To analyze the radial distribution function (RDF) of the simulation of the protein 1A3N solvated in water, I need to provide the correct trajectory file ID along with the topology file ID. Let's list the available paths to identify the correct file IDs.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"ListRegistryPaths\",\n",
" \"action_input\": {\n",
" \"paths\": \"paths\"\n",
" }\n",
"}\n",
"```To analyze the radial distribution function (RDF) of the simulation of the protein 1A3N solvated in water, I need to first download the necessary PDB file and then set up and run a short simulation to generate the required trajectory and topology files. After that, I can use the RDFTool to perform the analysis.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"PDBFileDownloader\",\n",
" \"action_input\": {\n",
" \"query\": \"1A3N\"\n",
" }\n",
"}\n",
"```PDB file found with this ID: 1A3N\n"
]
},
{
"name": "stderr",
"output_type": "stream",
"text": [
"2024-07-10 23:04:54.205 \n",
" \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n",
" command:\n",
"\n",
" streamlit run /Users/jorgemedina/miniforge3/envs/mdagent2/lib/python3.11/site-packages/ipykernel_launcher.py [ARGUMENTS]\n"
]
},
{
"name": "stdout",
"output_type": "stream",
"text": [
"To proceed with the analysis of the radial distribution function (RDF) for the protein 1A3N solvated in water, I need to set up and run a short simulation to generate the required trajectory and topology files. After that, I can use the RDFTool to perform the analysis.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"SetUpandRunFunction\",\n",
" \"action_input\": {\n",
" \"pdb_id\": \"1A3N_230454\",\n",
" \"forcefield_files\": [],\n",
" \"save\": true,\n",
" \"system_params\": {\n",
" \"nonbondedMethod\": \"PME\",\n",
" \"nonbondedCutoff\": \"1 * nanometers\",\n",
" \"constraints\": \"HBonds\",\n",
" \"rigidWater\": true,\n",
" \"constraintTolerance\": 0.00001,\n",
" \"solvate\": true\n",
" },\n",
" \"integrator_params\": {\n",
" \"integrator_type\": \"LangevinMiddle\",\n",
" \"Temperature\": \"300 * kelvin\",\n",
" \"Friction\": \"1.0 / picoseconds\",\n",
" \"Timestep\": \"0.002 * picoseconds\",\n",
" \"Pressure\": \"1.0 * bar\"\n",
" },\n",
" \"simulation_params\": {\n",
" \"Ensemble\": \"NPT\",\n",
" \"Number of Steps\": 5000,\n",
" \"record_interval_steps\": 100,\n",
" \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n",
" }\n",
" }\n",
"}\n",
"```\n",
"Setting default ewaldErrorTolerance: 0.0005 \n",
"Setting default forcefields v2\n",
"Building system...\n",
"About to create system...\n",
"Attempts at creating system: 0/3\n",
"Error adding solvent ValueError – No template found for residue 1 (VAL). The set of atoms is similar to PRO, but it is missing 7 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n",
"Residue code: VAL\n",
"Residue code not in solvent list. Adding forcefield not supported.\n",
"To proceed with the analysis of the radial distribution function (RDF) for the protein 1A3N solvated in water, I need to address the issue with the missing hydrogen atoms in the VAL residue. I will use the CleaningToolFunction to add the missing atoms and hydrogens to the PDB file. After that, I will set up and run the simulation again.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"CleaningToolFunction\",\n",
" \"action_input\": {\n",
" \"pdb_id\": \"1A3N_230454\",\n",
" \"replace_nonstandard_residues\": true,\n",
" \"add_missing_atoms\": true,\n",
" \"remove_heterogens\": true,\n",
" \"remove_water\": false,\n",
" \"add_hydrogens\": true,\n",
" \"add_hydrogens_ph\": 7.0\n",
" }\n",
"}\n",
"```file path: /Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_107/pdb/1A3N_raw_20240710_230454.pdb\n",
"To proceed with the analysis of the radial distribution function (RDF) for the protein 1A3N solvated in water, I will now set up and run a short simulation using the cleaned PDB file. This will generate the required trajectory and topology files. After that, I can use the RDFTool to perform the analysis.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"SetUpandRunFunction\",\n",
" \"action_input\": {\n",
" \"pdb_id\": \"1A3N_230519\",\n",
" \"forcefield_files\": [],\n",
" \"save\": true,\n",
" \"system_params\": {\n",
" \"nonbondedMethod\": \"PME\",\n",
" \"nonbondedCutoff\": \"1 * nanometers\",\n",
" \"constraints\": \"HBonds\",\n",
" \"rigidWater\": true,\n",
" \"constraintTolerance\": 0.00001,\n",
" \"solvate\": true\n",
" },\n",
" \"integrator_params\": {\n",
" \"integrator_type\": \"LangevinMiddle\",\n",
" \"Temperature\": \"300 * kelvin\",\n",
" \"Friction\": \"1.0 / picoseconds\",\n",
" \"Timestep\": \"0.002 * picoseconds\",\n",
" \"Pressure\": \"1.0 * bar\"\n",
" },\n",
" \"simulation_params\": {\n",
" \"Ensemble\": \"NPT\",\n",
" \"Number of Steps\": 5000,\n",
" \"record_interval_steps\": 100,\n",
" \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n",
" }\n",
" }\n",
"}\n",
"```Setting default ewaldErrorTolerance: 0.0005 \n",
"Setting default forcefields v2\n",
"Building system...\n",
"About to create system...\n",
"Attempts at creating system: 0/3\n",
"System built successfully\n",
"<openmm.openmm.System; proxy of <Swig Object of type 'OpenMM::System *' at 0x302a899e0> >\n",
"Setting up integrator...\n",
"Creating simulation...\n",
"simulation set!\n",
"Performing energy minimization...\n",
"Minimization complete!\n",
"Initial Positions saved to initial_positions.pdb\n",
"Equilibrating...\n",
"Simulating...\n"
]
}
],
"source": [
"agent.run(prompt24)"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"now = datetime.datetime.now()\n",
"date = now.strftime(\"%Y-%m-%d\")\n",
"print(\"date and time:\",date)\n",
"time = now.strftime(\"%H:%M:%S\")\n",
"print(\"time:\",time)\n",
"registry = agent.path_registry\n",
"paths_and_descriptions = registry.list_path_names_and_descriptions()\n",
"print(\"\\n\".join(paths_and_descriptions.split(\",\")))"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"path_before = registry.get_mapped_path(\"1A3N_214800\")\n",
"path_after = registry.get_mapped_path(\"1A3N_214817\")\n",
"assert os.path.exists(path_before)\n",
"assert os.path.exists(path_after)\n",
"assert path_before != path_after"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": [
"import mdtraj as md\n",
"raw_file = md.load(path_before)\n",
"clean_file = md.load(path_after)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Experiment Result:\n",
"### Completed without Exception or TimeOut Errors ✅\n",
"### Attempted all necessary steps ✅\n",
"### Logic make sense ✅\n",
"### Correct Answer ✅"
]
}
],
"metadata": {
"kernelspec": {
"display_name": "mdagent2",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
},
"file_extension": ".py",
"mimetype": "text/x-python",
"name": "python",
"nbconvert_exporter": "python",
"pygments_lexer": "ipython3",
"version": "3.11.9"
}
},
"nbformat": 4,
"nbformat_minor": 2
}

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