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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Received on Sun Oct 22 2006 - 06:07:29 PDT
