AMBER Archive (2005)

Subject: Re: AMBER: leap problem: savepdb

From: David A. Case (case_at_scripps.edu)
Date: Fri May 20 2005 - 10:21:13 CDT

On Fri, May 20, 2005, Hannes Barsch wrote:
>
> When saving a PDB file from leap my atom names are messed up. Below I have
> pasted the output of the desc commant within tleap and the same atoms
> grepped out of the PDB file when saved with savepdb. I had loaded
> leaprc.ff99 and leaprc.gaff (using AMBER 8) and there is no addPdbAtomMap
> entry for H[B,D,G][2,3]. Is this a bug or is this meant to be like this?

It's meant to be like this, because that is what the PDB standard wants.
There are a complicated set of rules for atom names, roughly boiling down to
this:

a. the element name is _right_ justified in the first two columns
b. extra letters may be added to distinguish different sites
c. if two protons are connected to the same heavy atom, then the number
    that distinguishes the two is placed in column 1 (go figure, although
    it really derives from the limitation to four characters for atom names.

So, you should think of what is in the pdb file as an encoding of the real
(IUPAC) atom name. The "desc" command gives the "real" name (which is used
internally in Amber), and the PDB file shows the encoded name.

Ambpdb has an option to not do this encoding, but programs that read pdb files
should be able to handle the example you give below.

...dac

> > desc pep.2
> RESIDUE name: PRO
> RESIDUE sequence number: 2
> RESIDUE PDB sequence number: 2
> Type: protein
> Connection atoms:
> Connect atom 0: A<N 1>
> Connect atom 1: A<C 13>
> Improper torsions:
> Contents:
> A<O 14>
> A<C 13>
> A<HA 12>
> A<CA 11>
> A<HB3 10>
> A<HB2 9>
> A<CB 8>
> A<HG3 7>
> A<HG2 6>
> A<CG 5>
> A<HD3 4>
> A<HD2 3>
> A<CD 2>
> A<N 1>
>
>
> [hbarsch_at_barsch Leap]$ grep 'PRO 2' leap.pdb
> ATOM 51 N PRO 2 4.908 -1.464 -2.158 1.00 0.00
> ATOM 52 CD PRO 2 5.837 -1.132 -3.232 1.00 0.00
> ATOM 53 2HD PRO 2 6.386 -0.227 -2.971 1.00 0.00
> ATOM 54 3HD PRO 2 5.282 -0.966 -4.155 1.00 0.00
> ATOM 55 CG PRO 2 6.722 -2.341 -3.306 1.00 0.00
> ATOM 56 2HG PRO 2 7.745 -2.020 -3.502 1.00 0.00
> ATOM 57 3HG PRO 2 6.388 -2.998 -4.109 1.00 0.00
> ATOM 58 CB PRO 2 6.605 -3.025 -1.965 1.00 0.00
> ATOM 59 2HB PRO 2 7.496 -2.814 -1.375 1.00 0.00
> ATOM 60 3HB PRO 2 6.517 -4.101 -2.118 1.00 0.00
> ATOM 61 CA PRO 2 5.344 -2.490 -1.229 1.00 0.00
> ATOM 62 HA PRO 2 4.670 -3.346 -1.235 1.00 0.00
> ATOM 63 C PRO 2 5.448 -1.937 0.186 1.00 0.00
> ATOM 64 O PRO 2 5.118 -0.779 0.428 1.00 0.00
>
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