On Mon, Mar 30, 2026, ElBagoury, Abdulrahman Walid Attia Ibrahim via AMBER wrote:
>However, when I use the PDB file that contains the docked ligand (after
>removing the original ligand), I encounter errors such as missing chains
>or missing residues. Interestingly, when I use the original unmodified PDB
>file, everything works correctly without errors.
It is indeed difficult to know what might have happened during the MOE
preparation. We would need to see details of the error messages you
received to be of much help. These messages might also point to genuine
problems with the initial PDB file, in terms of how well it is suited for MD
simulation.
>To work around this issue, I used PyMOL to copy the docked ligand
>coordinates and insert them into the original unmodified PDB
>structure. This way, I keep the original protein structure intact while
>replacing only the ligand coordinates.
This sounds like a reasonable approach to me. You have not said what you
intend to do with this docked structure, so it is hard to give detailed
advice.
...good luck...dac
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Received on Mon Mar 30 2026 - 08:00:04 PDT
