AMBER Archive (2009)

Subject: Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last

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• In reply to: Workalemhu Berhanu: "[AMBER] Unknown residue: MOL number: 30 type: Terminal/last"
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On Mon, Jun 08, 2009, Workalemhu Berhanu wrote:

> I am new user of amber. I created my ligand and peptide complex using
> PatchDock (Nucl. Acids. Res. 33: W363-367, 2005). When I used tleap for
> my ligand and peptide complex (which I named as solution.pdb) I got
> the errors shown below.

> COM =loadpdb "solution.pdb"
> Loading PDB file: ./solution.pdb
> (starting new molecule for chain B)
> (starting new molecule for chain D)
> (starting new molecule for chain )
> Unknown residue: MOL number: 30 type: Terminal/last

Looks like your ligand is named "MOL", and LEaP doesn't know anything about
such molecules. You will need to use antechamber to create a library file for
the ligand. See tutorial B4, plus the Users' Manual.

...dac

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• Previous message: moitrayee_at_mbu.iisc.ernet.in: "[AMBER] unit of charge in prep files"
• In reply to: Workalemhu Berhanu: "[AMBER] Unknown residue: MOL number: 30 type: Terminal/last"
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