AMBER Archive (2006)

Subject: AMBER: atom type nh vs. n2

From: sethl_at_gatech.edu
Date: Fri Oct 20 2006 - 16:31:09 CDT

Dear Amber Community,

I used antechamber/gaff to parameterize a proflavine molecule and am seeing some
curious behavior with the amine groups on each end of the molecule. Looking at
the definitions in the gaff.dat, it seems like the atom types should be type
"nh" but should they be "n2" instead? Here is my prep file:

molecule.res
UNK INT 0
CORRECT OMIT DU BEG
  0.0000
   1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
   2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
   3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
   4 N na M 3 2 1 1.540 111.208 180.000 -0.18558
   5 H hn E 4 3 2 1.021 95.506 -57.983 0.31847
   6 C2 ca M 4 3 2 1.266 22.672 116.670 0.15968
   7 C1 ca M 6 4 3 1.336 119.993 -6.160 -0.32433
   8 H1 ha E 7 6 4 1.100 120.005 0.622 0.15696
   9 C ca M 7 6 4 1.337 120.040 -179.425 0.30756
  10 N1 nh B 9 7 6 1.265 119.982 -179.971 -0.83020
  11 H8 hn E 10 9 7 1.051 119.952 -179.936 0.45664
  12 H9 hn E 10 9 7 1.050 120.040 -0.056 0.45381
  13 C5 ca M 9 7 6 1.337 119.973 0.028 -0.20655
  14 H3 ha E 13 9 7 1.099 120.000 179.935 0.16413
  15 C4 ca M 13 9 7 1.337 120.017 -0.002 -0.01056
  16 H2 ha E 15 13 9 1.100 120.034 179.981 0.16057
  17 C3 ca M 15 13 9 1.338 119.978 -0.024 -0.18037
  18 C8 ca M 17 15 13 1.338 119.978 179.464 0.08614
  19 H4 ha E 18 17 15 1.100 121.302 -0.543 0.16636
  20 C7 ca M 18 17 15 1.389 117.328 179.509 -0.18041
  21 C6 ca M 20 18 17 1.337 118.611 1.566 0.15970
  22 C9 ca M 21 20 18 1.337 119.940 178.254 -0.32427
  23 H5 ha E 22 21 20 1.100 119.986 -179.407 0.15696
  24 C10 ca M 22 21 20 1.337 120.010 0.675 0.30757
  25 N2 nh B 24 22 21 1.266 119.991 -178.996 -0.83020
  26 H10 hn E 25 24 22 1.050 120.015 -179.970 0.45666
  27 H11 hn E 25 24 22 1.050 120.037 -0.090 0.45379
  28 C11 ca M 24 22 21 1.337 120.048 0.890 -0.20659
  29 H6 ha E 28 24 22 1.100 120.123 177.944 0.16412
  30 C12 ca M 28 24 22 1.338 119.923 -2.026 -0.01059
  31 H7 ha E 30 28 24 1.100 119.964 -178.461 0.16055

LOOP
   C6 N
   C3 C2
  C12 C7

IMPROPER
   C6 C2 N H
   C3 C1 C2 N
   C2 C C1 H1
   C5 C1 C N1
    C H8 N1 H9
   C4 C C5 H3
   C5 C3 C4 H2
   C4 C8 C3 C2
   C3 C7 C8 H4
   C8 C6 C7 C12
   C7 C9 C6 N
   C6 C10 C9 H5
   C9 C11 C10 N2
  C10 H10 N2 H11
  C10 C12 C11 H6
   C7 C11 C12 H7

DONE
STOP

Thanks for the help,
SETH
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