On Sat, Jul 27, 2013, mohit mazumder wrote:
> Leap Log :
>
> Mapped residue DA, term: Terminal/last, seq. number: 18 to: DA3.
> Created a new atom named: P within residue: .R<DG5 2>
> Created a new atom named: O1P within residue: .R<DG5 2>
> Created a new atom named: O2P within residue: .R<DG5 2>
>
>
> Portion of the coordinate file.
>
> ATOM 1 P DG E 2 20.033 33.989 57.610 1.00 96.81
> ATOM 2 C5' DG E 2 19.959 31.904 59.296 1.00 94.96
> ATOM 3 O5' DG E 2 19.301 33.045 58.694 1.00 94.65
> ATOM 4 C4' DG E 2 19.452 31.465 60.686 1.00 93.99
> ATOM 5 O4' DG E 2 20.195 32.078 61.779 1.00 91.76
By default, Amber does not put phosphate groups on the 5' terminal ends of
nucleic acids: it makes the first residue in each chain a DG5 instead of DG.
To change this, you need to make a copy of the leaprc.ff12SB file, and edit
the line in addPdbResMap from { 0 "G" "G5" } to { 0 "G" "G" } . I haven't
done this in a while, and it may be necessary to build a terminal hydoxyl
group as well, probably renaming one of the oxygens attached to P to the O
of an OHE residue. If the fourth oxygen is not in your PDB file (did you give
all the "created new atom" records above?), you will have to build it
manually, and make it into a OHE residue.
Of course: be sure you really want the 5' phosphate! That is, that it is
really present in the relevant structure. Some (many?) Amber users take an
easier path and just remove those atoms.
...dac
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Received on Sat Aug 10 2013 - 07:00:03 PDT
