Re: AMBER: tleap BUG to write a pdb file if atom name contains 4 chars.

From: David A. Case <>
Date: Wed, 5 Jul 2006 18:54:38 -0700

On Wed, Jul 05, 2006, Christophe Guilbert wrote:

> Now follow some of the H atom type like "HN22" in my original pdb file
> "liga_regul.pdb" line 9.
> This atom type name is correctly defined in "lig_bcc.mol2" (output of
> Antechamber) line 15.
> the problem is in "liga_leap.pdb" (output of Tleap) , there is no atom
> type "HN22" anymore but it is called "2HN2" line 7

This is the behavior I would expect, and I think it is not a bug. If you
look at "real" PDB files (from that have hydrogens in them,
you will see that atom names like "2HN2" are there, but never anything like
"HN22". [The way I explain this is that the "real" name (the "Amber" name)
is "HN22", but the Brookhaven encoding of this name is "2HN2".]

The reason is what I tried to explain earlier: the "H" *must* be in column
14 (not column 13) in order to satisfy PDB format requirements. But, the
entire atom name must be in columns 13-16. So, no four-character name of
a hydrogen would ever fit both requirements. The "solution" (chosen by PDB,
not by me) is to place the fourth character of the atom name into column
13 (we call this "wrapping" in the code).

Programs that write PDB files have to perform this "wrapping" to satisfy the
format requirements (i.e they have to make the conversion HN22 -> 2HN2);
programs that read PDB files have to "un-wrap" the atom names (convert 2HN2 ->
HN22). If LEaP were to write the file the way you seem to prefer, programs
like RasMol would read such files incorrectly.

I hope you read the material on p. 284 of the Users' Manual, as it discusses
this point in more detail. Some programs require pretty strict adherence
to the official PDB format, and other programs are more leniant. What tleap
puts out looks correct to me.


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Received on Sun Jul 09 2006 - 06:07:10 PDT
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