Re: [AMBER] Problem with PDB files in LEaP

From: Daniel Roe <>
Date: Fri, 28 Jun 2013 10:43:31 -0600


On Fri, Jun 28, 2013 at 9:09 AM, Hunter Brown <> wrote:
> Leap added 1299 missing atoms according to residue templates:
> 55 Heavy
> 1244 H / lone pairs
> The file contained 1962 atoms not in residue templates
> When I check the file I get a bunch of FATAL messages saying that "ATOM _____ does not have a type." Almost 2000 of these in fact....

This means that leap was not able to match up atom names found in your
PDB with the atom names that leap has in residue templates. To explain
this, you need to know a little more about how leap tries to set up
your system. When you load a force field into leap, e.g. via:

$> source leaprc.ff10

leap loads a bunch of templates (in leap they are called 'Units')
which tells it how to recognize residues etc (you can see what Units
are loaded by typing 'list'). The 'desc' command can be used to
describe what is in a given Unit. For example, this is the template
for protein non-terminal glycine (GLY):

$> > desc GLY.1
RESIDUE sequence number: 1
RESIDUE PDB sequence number: 0
Type: protein
Connection atoms:
 Connect atom 0: A<N 1>
 Connect atom 1: A<C 6>
Improper torsions:
A<N 1>
A<H 2>
A<CA 3>
A<HA2 4>
A<HA3 5>
A<C 6>
A<O 7>

So when leap encounters a residue named GLY in e.g. your PDB, it looks
for atoms named N, H, CA, HA2, HA3, C, and O and matches them up with
the template. This is so leap knows how the atoms are connected, what
the atom types are, etc. However, problems occur if you have atoms
with non-standard names. Say for some reason you had a glycine in your
PDB with some non-standard atom names:

ATOM 105 N GLY A 7 -1.264 -7.970 0.384 1.00 0.00 N
ATOM 106 CA GLY A 7 -0.160 -8.111 1.339 1.00 0.00 C
ATOM 107 C GLY A 7 0.656 -6.840 1.602 1.00 0.00 C
ATOM 108 O GLY A 7 1.564 -6.899 2.431 1.00 0.00 O
ATOM 109 H GLY A 7 -2.197 -7.857 0.747 1.00 0.00 H
ATOM 110 HA1 GLY A 7 -0.543 -8.470 2.292 1.00 0.00 H
ATOM 111 HA2 GLY A 7 0.535 -8.859 0.962 1.00 0.00 H

HA1 is not an atom in the GLY template that leap has, so it will
create a new atom in that GLY with name HA1 (but it won't have a type
etc) and also add the missing 'HA3' since leap expects it to be there.

So what I suspect is happening here is your PDB has non-standard atom
names for certain residues. If you send me (off-list) your PDB I can
take a quick look at it.


Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-9119 (Fax)
AMBER mailing list
Received on Fri Jun 28 2013 - 10:00:02 PDT
Custom Search