AMBER Archive (2006)

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

From: Andy Purkiss (a.purkiss_at_mail.cryst.bbk.ac.uk)
Date: Tue May 30 2006 - 13:18:58 CDT

On Tue, 2006-05-30 at 10:36 -0700, David A. Case wrote:
> 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.
>

I think NAD (and it's relatives) break the normal pdb format. As they
have two ring systems separated a phosphate, the rings are distinguished
with A (for adenino) and N (for Nicotinamide) prefixes (see pdb file
1o9j for my example). This allows the pdb file to use separate the two
types of C4* for example, whilst keeping the co-factor as a single
molecule. I sure there is a rule for these dinucleotides, but I don't
have it to hand.

The actual atom symbol for the atom concerned is kept in the last column
(76 I think) allowing software to deal with the 'funny' formatting.
Exactly this problem caused all sorts of trouble when I was making the
figures to go with the pdbfile!! I had large bits of the NAD in blue as
the software thought they were nitrogen, the rest being correctly
coloured (as A got ignored).

> ....dac
>
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|  Andy Purkiss, School of Crystallography, Birkbeck College, London  |
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