Re: [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type.

From: Jason Swails <>
Date: Wed, 28 Jan 2015 12:54:08 -0500

On Wed, 2015-01-28 at 18:01 +0100, Mahad Gatti Iou wrote:
> Hello everyone,
> I'm new to AMBER, so I was reading other emails about the same topic as
> well as the user guide to start learning a little bit more.
> Basically, I want to run a simulation with NAMD using AMBER force field.
> Apparently it is not possible to use VMD's PSFgen plugin to obtain the
> parameter file, so I'm learning how to do that through leap.
> So far so good, I'm following a tutorial as well.
> When I'm loading the molecule I found this error, I got that there's some
> problem around the names of the residues in the PDB file and how AMBER
> actually reads them but still I wasn't able to find any information about
> what RU5 (and in general the syntax) is.

RU5 is the (old old old) residue name of a 5'-terminal ribouracil
residue. If that helps, great, but I suspect it doesn't.

> Can I receive some help regarding this matter?

Residue names in the PDB file *must* match the residue names in the
corresponding residue libraries (inside $AMBERHOME/dat/leap/lib). These
follow the PDB standard for the most part, but each protomer or tautomer
(e.g., protonated carboxylic acids, or epsilon- vs. delta-protonated
histidine) has a separate name which must be changed in the PDB file to
get the desired tautomer.

I would also suggest trying the "pdb4amber" tool, which should help
prepare your PDB file for use with leap.

For anything more than that, you will need to provide a lot more details
(with a lot more specificity) if you want help. Simplify the problem as
much as possible, then give exact input and output rather than trying to
describe it.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 28 2015 - 10:00:02 PST
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