Dear users,
I'll be most thankful for any help in the following matter. While trying
to prepare the amber prmtop, inpcrd and lib files, I'm encountering a
missing parameter for bond and angles containing an atom that from a
first glance in the prep file does not appear in this file.
Warning:
Checking for bond parameters.
Could not find bond parameter for: C - o
Checking for angle parameters.
Could not find angle parameter: O - C - o
Could not find angle parameter: C - o - c
Could not find angle parameter: CT - C - o
There are missing parameters.
My prep file is:
This is a remark line
molecule.res
HPD 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 O7 o M 3 2 1 1.540 111.208 180.000 -0.514169
5 C5 c M 4 3 2 1.382 78.099 141.003 0.375030
6 H7 h4 E 5 4 3 1.104 114.259 141.288 0.073892
7 C4 c3 M 5 4 3 1.540 117.068 10.630 0.024987
8 H6 hc E 7 5 4 1.095 108.811 92.756 0.026696
9 H8 hc E 7 5 4 1.099 109.619 -151.850 0.026696
10 C3 c3 M 7 5 4 1.543 111.787 -28.310 0.209274
11 O6 oh S 10 7 5 1.427 111.423 -34.571 -0.724771
12 H5 ho E 11 10 7 0.994 101.306 61.863 0.468108
13 H4 h1 E 10 7 5 1.103 108.019 85.218 0.030173
14 C2 c3 M 10 7 5 1.533 112.436 -155.467 0.130709
15 O5 oh S 14 10 7 1.424 111.788 -55.878 -0.640783
16 H3 ho E 15 14 10 0.973 108.111 -62.799 0.421852
17 H2 h1 E 14 10 7 1.095 109.045 59.666 0.156297
18 C1 c3 M 14 10 7 1.530 110.989 178.596 0.021642
19 H1 h1 E 18 14 10 1.095 111.948 60.076 0.112251
20 H9 h1 E 18 14 10 1.089 110.708 -61.859 0.112251
21 O4 os M 18 14 10 1.455 109.206 -178.071 -0.448937
22 P1 p5 M 21 18 14 1.582 122.749 -89.179 1.387183
23 O2 o E 22 21 18 1.466 114.691 160.935 -0.653126
24 O1 os M 22 21 18 1.626 110.326 -53.281 -0.297627
25 O3 os M 24 22 21 1.601 60.262 103.616 -0.297627
LOOP
O3 P1
IMPROPER
C4 H7 C5 O7
DONE
STOP
The small o is O7 and the small c is C5 as they should be.
So, which atom is designated by capital C (C1?) ? I have tried checking
every c atom in my substrate by changing its type though with no luck.
Thanks a lot,
Arik
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Received on Fri Nov 18 2011 - 16:30:02 PST
