AMBER Archive (2008)

Subject: Re: AMBER: antechamber bug? produces incorrect NEWPDB.PDB file

From: David A. Case (
Date: Tue Oct 28 2008 - 12:41:45 CDT

On Tue, Oct 28, 2008, Robert Hanson wrote:
> When we run antechamber to create NEWPDB.PDB and prepin files and assign
> AMBER atom types it looks like the NEWPDB.PDB file has an incorrect format:
> ATOM 18 H141AB1 1 -3.716 15.524 32.652 0.041810
> ATOM 19 H142AB1 1 -5.014 15.668 31.441 0.044700
> ATOM 20 H143AB1 1 -5.014 16.722 32.876 0.034220
> Really our atom names here are "1H14" "2H14" "3H14" in the original PDB
> file:
> HETATM 61 1H14 AB1 X 1 -3.716 15.524 32.652 0.00
> H 0
> HETATM 62 2H14 AB1 X 1 -5.014 15.668 31.441 0.00
> H 0
> HETATM 63 3H14 AB1 X 1 -5.014 16.722 32.876 0.00
> H 0
> But something in antechamber is moving those prefix numbers into the
> alternate location field of NEWPDB.PDB
> Is this a known problem?

Short answer: yes, and you will either have to live with the new atom names or
edit the output files.

Longer answer:

Depends on how you define "problem". In the old (version 2) pdb format,
the atomic symbol was suppose to be right justified in the first two
characters of the atom name. So, the first two characters of all hydrogens
should begin " H". However, since there are only a total of four columns
available, the final digit (1,2 3 here) was "wrapped around" into the first
column (which had been blank), leading to entries like "1H14". In a sense,
the atom name was always "really" H141, but the old pdb encoded this as

The newer PDB code (version 3, aka wwPDB, aka "remediated") dispenses with the
requirement of right justification of element information, and hydrogen names
in the pdb now begin with the letter "H" (as one assumes God intended).

These "real" atom names (beginning with "H") have always been used internally
in Amber. Generally, we try to read in either version 2 or version 3 names,
and write out version 3 style names. Some codes have options to write out
either old-style or new-style names, but antechamber is not doing this. And
Amber as a whole is not 100% consistent with either the old or new styles,
although we are getting closer (to the new style) all the time.


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