Re: [AMBER] tLeap, Fatal: Atom does not have a type

From: David A Case <>
Date: Tue, 16 Feb 2021 08:13:40 -0500

On Mon, Feb 15, 2021, Alysia Mandato wrote:
>I get output in tleap which says that it "Created a new atom named: O01
>within residue ..."

To be more explicit, this means that there is an atom names O01 in your pdb
file which is not present in the residue library. It sounds like you have
very non-standard atom-naming in your PDB file, and you will need to fix
that, perhaps by hand....depends a lot on how you got the PDB file in the
first place.

>atoms in my structure on PyMol, and they are part of a phosphate backbone
>of my DNA strand. Maybe they should be different atom types?

They should indeed have different atom *names*. (Types are things that are
internal to Amber.)
>Should I add these atom types somehow to the lib file, or is there a way to
>rename the strange atom types to the typical phosphate backbone atoms (P,
>OP1, OP2)?

You should change the PDB file. Perhaps with a text editor? I'm attaching
a little perl script that just reads in a PDB file, allows you to make
modifications, then writes it back out. It's a life-saver for lots of
little tweaks that need to be made.


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Received on Tue Feb 16 2021 - 05:30:03 PST
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