Re: [AMBER] pdb error

From: Jason Swails <>
Date: Sun, 6 Feb 2011 09:44:26 -0500

This occurred for one of two reasons. It's important to understand the
difference between atom NAMES and atom TYPES. Atom NAMES are used in PDB
files and are supposed to indicate to people which atoms they are. For
example, the alpha-carbon of amino acids have the NAME CA in the current PDB
standard (and the beta carbon is CB, etc.). The atom TYPE is what Amber
uses to assign parameters.

Obviously, simulations shouldn't care if an atom is the alpha-carbon, but
rather should care that it has 3 bonded partners in an sp3 hybridized
configuration. Note that there's no such thing as *hybridization* or any
knowledge of electronic configuration, but it is a useful tool to assign
parameters. Thus, what leap needs is something to translate PDB atom NAMES
into atom TYPES that it understands.

This is where so-called "library" files come in. Library files are
*templates* that tells leap what atoms are in each residue (so residue names
must match from the PDB to the library file), which atoms are connected to
other atoms in the residue (and which ones connect to neighboring residues),
and which atom TYPE corresponds to each atom NAME. This is the key. You
need a library file whose atom NAMES match the names found in the PDB file
and assign known atom TYPES to them. This is what failed in your leap
script. The two reasons this could have happened is

1. You never created and/or loaded a library file (library files can either
be mol2, amber prep, or amber OFF files created by leap by the saveOFF

2. If you did load a library file (it doesn't look like you did), then the
atom NAMES in your PDB file do not match the atom NAMES in the library file,
so leap doesn't know what TYPE to assign to them.

This was a very verbose response to your issue whose simple solution would
have been "load the library file" or "make sure the atom names match the
template", but I was hoping to provide more insight into how leap works so
future errors become easier to debug on your own.

Also note here that I only described the role of the library file.
Parameter files are needed to provide leap with information about what each
atom TYPE is and how it behaves when bonded with other atom TYPEs. These
parameters are stored in the parm.dat files in $AMBERHOME/dat/leap/parm or
in an "frcmod" file that you create for your specific residue. Therefore,
each atom TYPE must be defined (with mass and non-bonded parameters) either
somewhere in the loaded parameter set OR in your frcmod file that you create
specifically for your residue.

Hope this helps,

On Sun, Feb 6, 2011 at 12:27 AM, subrata paul <>wrote:

> Dear amber user
> We want to make urea molecule considering duffy model. for this first we
> make lib file and frcmod file.
> After loading the lib file ,we saved the molecule as pdb. then we want to
> save prmtop and inpcrd file from that pdb .
> u1=loadpdb ure.pdb
> saveamberparm u1 u1.prmtop u1.inpcrd
> FATAL: Atom .R <URE 1> .A<H1 1> does not have atype
> FATAL: Atom .R <URE 1> .A<H2 2> does not have atype
> FATAL: Atom .R <URE 1> .A<H3 3> does not have atype
> FATAL: Atom .R <URE 1> .A<H4 4> does not have atype
> FATAL: Atom .R <URE 1> .A<C 5> does not have atype
> FATAL: Atom .R <URE 1> .A<O 6> does not have atype
> FATAL: Atom .R <URE 1> .A<N1 7> does not have atype
> FATAL: Atom .R <URE 1> .A<N2 8> does not have atype
> Failed to generate parameters
> parameter files are not generate
> Why it comes as this?
> please help me
> thanking you
> subrata
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Sun Feb 06 2011 - 07:00:06 PST
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