Dear [Recipient Name / AMBER Support],
I am experiencing a recurring issue with MCPB.py. I am trying to generate
the bonded model files for my Ru(II) complex, but the program repeatedly
returns the error:
pymsmtexp.pymsmtError: X pdb files provided for original_pdb, only need one.
I have followed the official tutorial (AMBER Tutorial 20
<
https://ambermd.org/tutorials/advanced/tutorial20/mcpbpy.php>) and tried
several approaches:
- Cleaning the PDB (grep -v '^MODEL|^ENDMDL' RU_COMPLEX.pdb >
RU_CLEAN.pdb)
- Updating mcpb.in to use RU_CLEAN.pdb
- Ensuring ion_ids corresponds to the correct Ru atom number
- Removing previously generated PDB and log files
Despite these steps, MCPB still detects multiple PDB files and fails to run.
Could you please help me understand what causes this error and how to
properly prepare my PDB file for MCPB? My goal is to generate a bonded
model for my Ru(II) complex with charge +2 and multiplicity 1.
Thank you very much for your time and assistance.
Best regards,
Prof. Abdelatif Messaoudi
LCMVAR Laboratory, University of Batna 1, Algeria
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Received on Fri Apr 03 2026 - 08:30:03 PDT
