[AMBER] DNA Phosphate error

From: mohit mazumder <mohitmazumder.gmail.com>
Date: Sat, 27 Jul 2013 12:06:17 +0530

Hello all,

>From the past few days I am trying to obtain topology for a DNA-Protein
complex.

The problem is with the phosphate of DNA as leap is not able to recognize
it.

Earlier I thought that there is a problem with the naming nomenclature. As
I browse through the previous posts.

The problem is : instead of treating P as a heavy atom , it is creating new.

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.
Coordinate file :

ATOM 1 P DG E 2 20.033 33.989 57.610 1.00 96.81
  P
ATOM 2 C5' DG E 2 19.959 31.904 59.296 1.00 94.96
  C
ATOM 3 O5' DG E 2 19.301 33.045 58.694 1.00 94.65
  O
ATOM 4 C4' DG E 2 19.452 31.465 60.686 1.00 93.99
  C
ATOM 5 O4' DG E 2 20.195 32.078 61.779 1.00 91.76
  O
ATOM 6 C3' DG E 2 17.998 31.727 61.086 1.00 95.61
  C
ATOM 7 O3' DG E 2 17.669 30.886 62.181 1.00 99.64
  O
ATOM 8 C2' DG E 2 18.080 33.148 61.609 1.00 92.63
  C
ATOM 9 C1' DG E 2 19.335 32.986 62.452 1.00 87.72
  C
ATOM 10 N1 DG E 2 23.313 35.116 64.526 1.00 83.13
  N
ATOM 11 C2 DG E 2 22.826 33.836 64.636 1.00 84.98
  C
ATOM 12 N2 DG E 2 23.506 32.988 65.425 1.00 83.21
  N
ATOM 13 N3 DG E 2 21.745 33.408 64.014 1.00 84.18
  N
ATOM 14 C4 DG E 2 21.195 34.388 63.278 1.00 84.98
  C
ATOM 15 C5 DG E 2 21.584 35.690 63.085 1.00 83.53
  C
ATOM 16 C6 DG E 2 22.747 36.126 63.756 1.00 84.71
  C
ATOM 17 O6 DG E 2 23.282 37.235 63.735 1.00 84.00
  O
ATOM 18 N7 DG E 2 20.705 36.346 62.223 1.00 85.86
  N
ATOM 19 C8 DG E 2 19.823 35.428 61.928 1.00 85.50
  C
ATOM 20 N9 DG E 2 20.067 34.226 62.546 1.00 85.65
  N
ATOM 21 O1P DG E 2 21.422 33.519 57.377 1.00 95.67
  O
ATOM 22 O2P DG E 2 19.124 34.196 56.455 1.00 94.43
  O1-

Is there some problem with my installation or some bug ??

I tried to obtain parameters using two different machines but yielded the
same error.

I tried different forcefields as well.

Can someone explain what I am missing here?

Attached : leap.log and the DNA coordinates.

Regards
Mohit Mazumder
PhD


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Received on Sat Jul 27 2013 - 00:00:02 PDT
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