That is very strange. Can you send both your RU_CLEAN.pdb file and mcpb.in file?
> On Apr 3, 2026, at 10:26 AM, ABDELATIF MESSAOUDI via AMBER <amber.ambermd.org> wrote:
>
> 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 Wed Apr 08 2026 - 19:30:03 PDT
