AMBER Archive (2009)
Subject: Re: [AMBER] Unknown residue: MOL number: 30 type: Terminal/last
From: David A. Case (case_at_biomaps.rutgers.edu)
Date: Tue Jun 09 2009 - 06:51:42 CDT
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.
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