AMBER Archive (2006)

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

From: Christophe Guilbert (cguilbert_at_picasso.ucsf.edu)
Date: Wed Jul 05 2006 - 21:50:24 CDT

Ok thanks for the explanation.
Actually, I am not an Amber user but a real fan of Antechamber ! I was
just disturbed by the fact that the topology file and the pdb file (both
generated by tleap) could have different atom type name. "2HN2" in the
pdb file and "HN22" in Amber topology file (%FLAG ATOM_NAME section).
Sorry for the fuzz.
Chris

David A. Case wrote:

>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 www.rscb.org) 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.
>
>....dac
>
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