AMBER Archive (2006)

Subject: Re: AMBER: SAVEPDB in Xleap could not save 4 character atom names

From: David A. Case (case_at_scripps.edu)
Date: Tue May 30 2006 - 12:36:37 CDT

On Mon, May 29, 2006, Jiayun Pang wrote:

> My initial NADH pdb is as the following
>
> ATOM 5577 NC1' NAD 600 12.002 47.794 20.133 1.00 23.51
> ATOM 5579 NC2' NAD 600 11.045 46.903 20.882 1.00 24.23
> ATOM 5581 NO2' NAD 600 11.638 46.538 22.126 1.00 24.05
> ATOM 5583 NC3' NAD 600 10.754 45.781 19.866 1.00 23.14
> ATOM 5586 NO4' NAD 600 11.690 47.609 18.722 1.00 24.57
> ATOM 5587 NC4' NAD 600 10.877 46.474 18.495 1.00 23.73
> ATOM 5589 NC5' NAD 600 9.514 46.772 17.900 1.00 22.66
> ..........................
> .........................
>
> where I have made sure that the atom names occupy column 13-16 and these atom
> names are directly taken from the PDB file in protein data banko

What is the pdb code for this system? I didn't know that such names
were allowed (i.e. with an "N" in column 13).

The PDB standard states that columns 13-14 should contain the atomic symbol
of the atom, *right* justified in those two columns. If the resulting column
13 is blank (as it will be for one-character atomic symbols), pdb allows a
an additional identifer to replace the space. This is usually just 1,2, or 3,
to specify hydrogen positions.

The problem is that many "pdb" files (created by Amber and other programs)
don't follow this convention, and left justify the entire atom name in cols.
13-16. If you don't know what kind of pdb file you have, you can't tell
if an atom named "NO4'" is a nitrogen or an oxygen.

Anyway, we have not run across files like this before, and we may have to
change our code to (try to) accommodate them. In the meantime, as another
poster suggested, you will probably have to replace the "N" in column 13 with
a blank.

....dac

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