AMBER Archive (2009)

Subject: Re: [AMBER] About the "FATAL: Atom err"!

From: case (case_at_biomaps.rutgers.edu)
Date: Mon Jun 22 2009 - 06:47:59 CDT

On Mon, Jun 22, 2009, Aurum Bai wrote:

Please only post once.

> I follow the protocol "http://ringo.ams.sunysb.edu/index.php/AMBER_tutorial"
>
> When do the "check oxy" procedure, some err happy as below:
>
> > check oxy
> Checking 'oxy'....
> WARNING: The unperturbed charge of the unit: 3.000000 is not zero.
> FATAL: Atom .R<PTR 683>.A<N 1> does not have a type.

You have a residue named "PTR" but the Amber libraries don't know about such
residues, only about standard ones. You must have loaded a different PDB
file than the one in the tutorial. See the tutorials at http://ambermd.org for
information on how to deal with non-standard residues.

...dac

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