Frequently Asked Questions
Why did my preparation crash?
An error in the preparation can have many reasons, the most frequent reasons are listed here:
- Residue numbers in the PDB file do not start at "1".
- Inconsistent atom or residue numbers in the PDB file.
- Unknown residue names. If the residue names provided in the PDB can not be recongized by pdb2gmx.
- Missing residues or loops in the receptor structure.
- Ligand that can not be protonated correctly using OpenBabel.
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