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Segmentation fault encountered using Interface

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Segmentation fault encountered using Interface

Hi All, 

I ran into repeated segmentation fault error when I tried to utilize the InterfaceAnalyzerMover to calcualte interaction energy between the two protein chains. 


Here is my script: 

import pyrosetta
from pyrosetta.rosetta.core.import_pose import pose_from_file
from pyrosetta.rosetta.protocols.analysis import InterfaceAnalyzerMover
import sys

def calculate_interface_energy(pdb_file, chain_target, chain_partners):
    Calculates the interaction energy between one chain and a complex formed by other chains in a protein structure.
        pdb_file (str): Path to the PDB file.
        chain_target (str): Identifier for the target chain.
        chain_partners (str): Identifiers for the partner chains concatenated.
        float: The interaction energy between the target chain and the partner chains.

    # Load the PDB file into a Pose object
    pose = pose_from_file(pdb_file)

    # Define the complex as a combination of the target chain and partner chains
    complex_identifier = chain_target + "_" + chain_partners

    # Setup the InterfaceAnalyzerMover for the defined complex
    interface_analyzer = InterfaceAnalyzerMover()
    interface_analyzer.test_move(pose)  # Test the move to ensure the interface is correctly defined
    interface_analyzer.apply(pose)  # Apply the mover to the pose

    # Retrieve the computed interface energy
    interface_energy = interface_analyzer.get_interface_dG()

    return interface_energy

def main():
    # Specify your parameters
    pdb_file = sys.argv[1]
    chain_target = "A"     # The single chain you are focusing on
    chain_partners = "B"  # The other chains, treated as a combined entity

    # Initialize PyRosetta
    pyrosetta.init(extra_options="-mute all -load_PDB_components false -extra_res_fa GDP.params")

    # Calculate and print the interface energy
    interface_energy = calculate_interface_energy(pdb_file, chain_target, chain_partners)
    print(f"Interface energy between chain {chain_target} and chains {chain_partners}: {interface_energy} REU")

if __name__=="__main__":


The seg-fault error happens with either test_move, or apply (when I comment out test_move) 

I can't figure out the problem because it seems to me that the error stems from the underlying C++ script. 

Any suggestion is appreciated. 


P.S. I cannot attach the test input I used because it is too big and this forum doesn't take the zipped version. If the error cannot be replicated with a different input, I will try to paste the PDB content as plain text in replies. 

Post Situation: 
Tue, 2024-04-02 13:41