Re: odd display of ambpdb generated files

From: David Case <>
Date: Tue 17 Apr 2001 12:33:16 -0700

On Tue, Apr 17, 2001, Bill Ross wrote:
> Actually, the PDB standard assigns the 13th column to be only
> occupied by a 2nd (wrapped) number on a hydrogen - the 14th is
> supposed to be the beginning of the element. If it isn't an H
> with the extra digit (HC12), there shouldn't be anything in 13.
> The atom name can extend to the residue # in the standard.

This thread is probably going the wrong direction. Please visit and go to "File formats and standards" to see the real
format requirements from PDB.

The atom name goes in columns 13-16; The (one or two character) element
name is *right* justified in columns 13 and 14; as Bill notes above, column
13 can also be used to hold a digit to help identify hydrogens. Note that
this is not just for names that would otherwise be four characters long.
For example, for example PHE will have an atom labelled " HD1" whereas
LYS will have an atom labelled "1HD ".

(I find it easiest to think of columns 13-16 in a pdb file as an "encoding"
of the atom name; in both cases above the atom name (IUPAC name) is "HD1",
and Brookhaven uses two different encodings for this name, depending upon
what residue it is in. Internally, amber uses IUPAC names.)

Column 17 is a "alternate location indicator" (generally for describing
disorder in crystals); columns 18-20 have the resiude name (not number). It
is not the case that the atom name can run into the residue name (for
properly formatted PDB files).

Among the amber programs, I believe that ambpdb with the -wrap option
comes closest to the standard. The next release of amber should be
better, and we will make an effort to have LEaP, ptraj, ambpdb and carnal
provide compatible outputs.....I recognize that there is more confusion
now than there should be.


David A. Case                     |  e-mail:
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
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Received on Tue Apr 17 2001 - 12:33:16 PDT
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