AMBER Archive (2009)

Subject: Re: [AMBER] fatal "does not have a type" error in tleap for a protein-ligand complex

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Sep 24 2009 - 17:13:39 CDT

On Thu, Sep 24, 2009, Jeff Yeo wrote:

>
> The "check MOL" command proceeded without errors or warnings (Unit is OK). However, the "loadpdb" command gave me the following messages:
> Loading PDB file: ./complex.pdb
> -- residue 278: duplicate [ H2] atoms (total 2)
> Warning: Atom names in each residue should be unique.
> (Same-name atoms are handled by using the first
> occurrence and by ignoring the rest.
> Frequently duplicate atom names stem from alternate
> conformations in the PDB file.)

This is pretty straightforward: you have two atoms, both named "H2" in the
ligand pdb file. You need to figure out why, and make all atom names inside
a residue unique.

> Created a new atom named: N25 within residue: .R<SUN 278>
> Added missing heavy atom: .R<SUN 278>.A<N2 33>

You have an atom named "N25" in the pdb file, but the prepi file doesn't have
any such atom. It's hard to see from your description why that happened, but
you need to examine closely the antechamber runs to see when and where the
N25 atom "disappeared."

> FATAL: Atom .R<SUN 278>.A<N25 37> does not have a type.

Since N25 is not in the prepi file, it does not have an atom type assigned.

...hope this helps....dac

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