47 lines
1.8 KiB
Python
47 lines
1.8 KiB
Python
from pathlib import Path
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import subprocess
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import os
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def generate_gmx_top_files(directory, num_cores, forcefield="amber99sb-ildn", water_model="tip3p"):
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"""
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Generate GROMACS topology (.top) files for each PDB file in the specified directory
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by running the 'gmx_mpi pdb2gmx' command in batch, with the working directory set to the specified directory.
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Args:
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directory (str): Directory containing PDB files.
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num_cores (int): Number of cores to use for mpirun.
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forcefield (str): Forcefield parameter for GROMACS. Default is "amber99sb-ildn".
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water_model (str): Water model parameter for GROMACS. Default is "tip3p".
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"""
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# Ensure the GMXRC path is sourced if set
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gmxrc_path = os.getenv("GMXRC_PATH")
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if gmxrc_path:
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subprocess.run(f"source {gmxrc_path}", shell=True, executable='/bin/bash')
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# Find all PDB files in the specified directory
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pdb_files = Path(directory).glob("*.pdb")
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# Iterate over each PDB file and execute the GROMACS command
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for pdb_file in pdb_files:
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name = pdb_file.stem # Extract the name without the '.pdb' extension
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output_gro = f"{name}.gro"
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topol_file = "topol.top"
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# Construct and run the command with the working directory set to 'directory'
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cmd = [
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"mpirun", "-np", str(num_cores),
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"gmx_mpi", "pdb2gmx",
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"-f", str(pdb_file),
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"-o", output_gro,
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"-ff", forcefield,
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"-water", water_model,
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"-ignh",
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"-p", topol_file
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]
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subprocess.run(cmd, check=True, cwd=directory)
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# Example usage
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directory = "pdb_top" # Replace with your actual directory path
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num_cores = max(os.cpu_count() - 2, 1) # Determine the number of cores to use
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generate_gmx_top_files(directory, num_cores) # Run the function
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