Re: [AMBER] FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type

From: David A Case <>
Date: Fri, 26 Sep 2014 11:54:02 -0400

On Fri, Sep 26, 2014, Soumendranath Bhakat wrote:

> FATAL: Atom .R<NLEU -1>.A<H 22> does not have a type.

To expand/simplify what Carlos said:

Your PDB file has a atom named "H" in the first resdidue. But the
IUPAC/PDB/Amber nomenclature for an N-terminal amino acid does not have any
such atoms: the three hydrogens bonded to the "N" atom are called H1, H2, and

So, the PDB atom names don't match the library atom names, and tleap doesn't
know what to do, and quits.

As Carlos said, the simplest thing to do is just to remove the "H" atom
from the PDB file. Another option is to use the "reduce" program first.
Even better would be to get in the habit of using "pdb4amber" before running


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Received on Fri Sep 26 2014 - 09:00:02 PDT
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