Hi,
I suggest you contact CCG support at support.chemcomp.com so we can help
you directly.
But a few notes:
Without looking at your PDB files and your bash script, I cannot say why
the original PDB file doesn't produce errors while the PDB of the docked
pose does.
It could be down to naming of the residues (MOE has an option to write PDB
files that conform to AMBER naming rather than IUPAC or RCSB naming), PDB
formats (the PDB format is sometimes too flexible for its own good), etc.
MOE writes PDB files that are faithful to the RCSB specifications and to
the system MOE: If your system has missing residues, then the created PDB
will have missing residues.
Please keep in mind, that MOE's QuickPrep protocol will only deal with
smaller missing gaps automatically:
If you have larger missing gaps, you will need to manually address these
since no structure preparation should be done blindly.
I would suggest that you do all the system preparation - dealing with
missing residues, setting protonation states etc - in one tool. If you run
docking in one tool, you should use the same protonation states for later
calculations, otherwise you might end up running MD on a docking pose that
doesn't have the same protonation states (think of e.g. His residues in the
binding pocket).
Kind regards,
Sarah
On Mon, Mar 30, 2026 at 8:49 AM ElBagoury, Abdulrahman Walid Attia Ibrahim
via AMBER <amber.ambermd.org> wrote:
> Hello ,
>
>
> I am currently working on a project that involves docking a ligand into an
> enzyme. I performed the docking using MOE, and afterward I used AMBER Tools
> for system preparation, including protonation, tleap setup, and running
> everything through Bash.
>
> 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.
>
> 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.
>
> I would like to know if this is a valid approach. If not, how can I
> properly fix the issue with the MOE-generated PDB file so that AMBER Tools
> can process it without errors?
>
>
>
>
> Abdulrahman Walid Attia Ibrahim ElBagoury
> Antivirale und Antivirulenz-Wirkstoffe
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Received on Mon Mar 30 2026 - 06:30:02 PDT
