AMBER Archive (2003)

Subject: growing side chains

From: Robert G. Endres (endresrg_at_ornl.gov)
Date: Mon Apr 07 2003 - 13:37:30 CDT

Dear AMBER users,

I have been trying to grow side chains with leap given the backbone atoms
and a residue template file, but when measuring the dihedreal angle
connecting the side chain with the backbone it is not the one from the
template.
To be more specific let's take for instance a thymine DNA base. First I
have a pdb file with just the nucleotide backbone atoms (atoms 4-15 and
30-35) and also base atom N9 (atom 16), as well as a template like
"DT.in":
------------------------------------------------------------------------
   0 0 2

D-THYMINE - with 5' - phosphate group and 3' - O(minus) group

 DT INT 1
 CORRECT OMIT DU BEG
   0.0
   1 DUMM DU M 0 -1 -2 0.00 0.00 0.00 0.0000
   2 DUMM DU M 1 0 -1 1.00 0.00 0.00 0.0000
   3 DUMM DU M 2 1 0 1.00 90.00 0.00 0.0000
   4 P P M 3 2 1 1.60 119.04 200.00 1.1659
   5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7761
   6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7761
   7 O5' OS M 4 3 2 1.60 101.43 -98.89 -0.4954
   8 C5' CT M 7 4 3 1.44 119.00 -39.22 -0.0069
   9 H5'1 H1 E 8 7 4 1.09 109.50 60.00 0.0754
  10 H5'2 H1 E 8 7 4 1.09 109.50 -60.00 0.0754
  11 C4' CT M 8 7 4 1.52 110.00 180.00 0.1629
  12 H4' H1 E 11 8 7 1.09 109.50 -200.00 0.1176
  13 O4' OS S 11 8 7 1.46 108.86 -86.31 -0.3691
  14 C1' CT B 13 11 8 1.42 110.04 105.60 0.0680
  15 H1' H2 E 14 13 11 1.09 109.50 -240.00 0.1804
  16 N9 N* S 14 13 11 1.53 109.59 -127.70 -0.0239
  17 C8 CM B 16 14 13 1.37 123.04 81.59 -0.2209
  18 H6 H4 E 17 16 14 1.08 120.00 0.00 0.2607
  19 C5 CM B 17 16 14 1.34 121.22 177.30 0.0025
  20 C7 CT 3 19 17 16 1.50 121.63 180.00 -0.2269
  21 H71 HC E 20 19 17 1.09 109.50 60.00 0.0770
  22 H72 HC E 20 19 17 1.09 109.50 180.00 0.0770
  23 H73 HC E 20 19 17 1.09 109.50 300.00 0.0770
  24 C4 C B 19 17 16 1.44 120.78 0.00 0.5194
  25 O4 O E 24 19 17 1.23 125.35 180.00 -0.5563
  26 N3 NA B 24 19 17 1.38 114.07 0.00 -0.4340
  27 H3 H E 26 24 19 1.09 116.77 180.00 0.3420
  28 C2 C S 26 24 19 1.38 126.46 0.00 0.5677
  29 O2 O E 28 26 24 1.22 121.70 180.00 -0.5881
  30 C3' CT M 11 8 7 1.53 115.78 -329.11 0.0713
  31 H3' H1 E 30 11 8 1.09 109.50 30.00 0.0985
  32 C2' CT B 30 11 8 1.53 102.80 -86.30 -0.0854
  33 H2'1 HC E 32 30 11 1.09 109.50 120.00 0.0718
  34 H2'2 HC E 32 30 11 1.09 109.50 240.00 0.0718
  35 O3' OS M 30 11 8 1.42 116.52 -203.47 -0.5232

CHARGE deoxy -resp T
  1.1659 -0.7761 -0.7761 -0.4954 -0.0069
  0.0754 0.0754 0.1629 0.1176 -0.3691
  0.0680 0.1804 -0.0239 -0.2209 0.2607
  0.0025 -0.2269 0.0770 0.0770 0.0770
  0.5194 -0.5563 -0.4340 0.3420 0.5677
 -0.5881 0.0713 0.0985 -0.0854 0.0718
  0.0718 -0.5232

IMPROPER
 C8 C2 N9 C1'
 C4 C8 C5 C7
 N9 N3 C2 O2
 C5 N3 C4 O4
 C2 C4 N3 H3
 N9 C5 C8 H6

LOOP CLOSING EXPLICIT
 C1' C2'
 C2 N9

DONE
STOP
---------------------------------------------------------
When xleap adds the missing atoms it prints:

  Added missing heavy atom: .R<DT 1>.A<C8 14>
  Added missing heavy atom: .R<DT 1>.A<C2 25>
  Added missing heavy atom: .R<DT 1>.A<C5 16>
  Added missing heavy atom: .R<DT 1>.A<N3 23>
  Added missing heavy atom: .R<DT 1>.A<O2 26>
  Added missing heavy atom: .R<DT 1>.A<C7 17>
  Added missing heavy atom: .R<DT 1>.A<C4 21>
  Added missing heavy atom: .R<DT 1>.A<O4 22>

My questions are the following:

First, the order of adding the atoms doesn't correspond to the order in
the DT.in file.

Second, when I measure the dihedral angle defined by C8 N9 C1' O4'
it is not 81.59 as specified in line 17 above through atoms 17 16 14 13
but deviates by a few degrees.

All this seems to work much better with amino acids, but I don't know why.
Any comments and insights are very appreciated!

Best regards,
  Robert