Hi, I tried to use antechamer for a HIV-PR inhibitor called MK1.
I successefully run the command:
antechamber -i MK1H.pdb -fi pdb -o mk1.prepi -fo prepi
Then I ran the pamrchk, the output of frcmod does not contain any warning
lines.
Then I used to leap to load in the mk1.prepi, and then try to load the
molecule MK1H.pdb, but the program died the minute I loaded the pdb file.
THe error message says:
FATAL: In file [atom.c], line 443
FATAL: Message: bondAtomProblem found
I attached the mk1.prepi below.
Could anyone help me?
contents of the mk1.prepi file follows:
0 0 2
This is a remark line
molecule.res
MK1 XYZ 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 C5 c3 M 3 2 1 1.540 111.208 180.000 -0.073
5 H hc E 4 3 2 1.097 117.767 147.112 0.028
6 H hc E 4 3 2 1.097 22.827 81.622 0.028
7 H hc E 4 3 2 1.097 84.823 -106.428 0.028
8 C4 c3 M 4 3 2 1.540 119.836 6.492 -0.054
9 C6 c3 3 8 4 3 1.386 110.376 -154.010 -0.073
10 H hc E 9 8 4 1.097 113.155 177.231 0.028
11 H hc E 9 8 4 1.098 111.841 -63.947 0.028
12 H hc E 9 8 4 1.098 113.560 55.951 0.028
13 C7 c3 3 8 4 3 1.466 104.558 -38.438 -0.073
14 H hc E 13 8 4 1.097 111.690 63.896 0.028
15 H hc E 13 8 4 1.096 112.743 -177.170 0.028
16 H hc E 13 8 4 1.098 113.124 -56.576 0.028
17 N2 n M 8 4 3 1.428 106.969 82.271 0.143
18 H hn E 17 8 4 1.016 114.014 6.569 0.025
19 C3 c M 17 8 4 1.319 130.352 -170.898 0.108
20 O1 o E 19 17 8 1.224 122.686 4.298 -0.307
21 C2 c3 M 19 17 8 1.505 116.974 -176.403 0.056
22 H h1 E 21 19 17 1.097 112.159 11.986 0.077
23 C1 c3 M 21 19 17 1.516 108.369 -110.760 -0.001
24 H h1 E 23 21 19 1.097 105.192 61.854 0.059
25 H h1 E 23 21 19 1.101 110.345 -49.512 0.059
26 N1 n3 M 23 21 19 1.488 121.344 -177.498 -0.309
27 C31 c3 3 26 23 21 1.468 117.247 -166.915 0.001
28 H h1 E 27 26 23 1.098 107.960 -176.047 0.063
29 H h1 E 27 26 23 1.098 108.709 -63.677 0.063
30 C32 ca S 27 26 23 1.533 121.388 63.136 -0.055
31 C33 ca B 30 27 26 1.402 123.063 75.877 -0.107
32 H h4 E 31 30 27 1.086 119.604 -3.568 0.069
33 N5 nb S 31 30 27 1.405 126.301 178.978 0.115
34 C34 ca B 33 31 30 1.394 110.783 -0.080 -0.114
35 H h4 E 34 33 31 1.087 114.054 -179.561 0.068
36 C35 ca B 34 33 31 1.398 125.815 0.106 -0.091
37 H ha E 36 34 33 1.088 119.274 -178.286 0.082
38 C36 ca S 36 34 33 1.393 119.896 -0.142 -0.078
39 H ha E 38 36 34 1.086 119.901 -178.781 0.084
40 C9 c3 M 26 23 21 1.394 107.347 62.224 -0.011
41 H h1 E 40 26 23 1.099 109.167 77.488 0.058
42 H h1 E 40 26 23 1.096 110.139 -167.017 0.058
43 C8 c3 M 40 26 23 1.515 116.382 -43.570 -0.010
44 H h1 E 43 40 26 1.098 105.606 -85.935 0.058
45 H h1 E 43 40 26 1.096 108.753 160.107 0.058
46 N3 n3 M 43 40 26 1.484 117.529 34.517 -0.300
47 C10 c3 M 46 43 40 1.449 109.063 -172.535 0.001
48 H h1 E 47 46 43 1.100 110.248 37.018 0.060
49 H h1 E 47 46 43 1.098 109.234 149.414 0.060
50 C11 c3 M 47 46 43 1.529 114.157 -91.429 0.032
51 H h1 E 50 47 46 1.096 110.099 46.774 0.083
52 O2 oh S 50 47 46 1.396 95.185 158.401 -0.438
53 H ho E 52 50 47 0.976 108.423 -104.116 0.273
54 C12 c3 M 50 47 46 1.540 124.151 -85.722 -0.032
55 H hc E 54 50 47 1.098 107.779 -57.584 0.038
56 H hc E 54 50 47 1.095 106.691 55.702 0.038
57 C13 c3 M 54 50 47 1.535 120.598 178.679 0.003
58 H hc E 57 54 50 1.097 106.102 60.123 0.052
59 C14 c3 3 57 54 50 1.539 112.253 179.498 -0.032
60 H hc E 59 57 54 1.097 109.712 -59.608 0.041
61 H hc E 59 57 54 1.098 109.082 55.919 0.041
62 C15 ca S 59 57 54 1.484 112.489 179.675 -0.058
63 C16 ca B 62 59 57 1.396 122.608 53.328 -0.077
64 H ha E 63 62 59 1.086 120.979 3.443 0.085
65 C17 ca B 63 62 59 1.387 120.641 -178.212 -0.083
66 H ha E 65 63 62 1.086 120.636 -179.681 0.084
67 C18 ca B 65 63 62 1.396 118.779 0.095 -0.084
68 H ha E 67 65 63 1.086 119.613 179.359 0.084
69 C19 ca B 67 65 63 1.400 120.774 -0.474 -0.083
70 H ha E 69 67 65 1.086 120.128 179.811 0.084
71 C20 ca S 69 67 65 1.395 119.768 0.444 -0.077
72 H ha E 71 69 67 1.087 118.858 179.684 0.085
73 C21 c M 57 54 50 1.524 112.087 -57.600 0.095
74 O3 o E 73 57 54 1.240 120.597 -48.558 -0.308
75 N4 n M 73 57 54 1.330 115.362 137.340 0.145
76 H hn E 75 73 57 1.015 122.066 -0.990 0.025
77 C22 c3 M 75 73 57 1.453 121.578 164.593 -0.006
78 H h1 E 77 75 73 1.098 109.024 -24.560 0.045
79 C23 c3 M 77 75 73 1.519 112.024 -145.045 0.028
80 H h1 E 79 77 75 1.095 110.590 83.623 0.082
81 O4 oh S 79 77 75 1.420 110.250 -33.508 -0.438
82 H ho E 81 79 77 0.976 107.148 174.897 0.273
83 C24 c3 M 79 77 75 1.511 105.233 -156.771 -0.018
84 H hc E 83 79 77 1.096 110.919 152.424 0.044
85 H hc E 83 79 77 1.096 110.224 -87.676 0.044
86 C25 ca M 83 79 77 1.509 110.643 31.073 -0.050
87 C26 ca M 86 83 79 1.375 137.314 159.603 -0.077
88 H ha E 87 86 83 1.085 120.988 1.768 0.085
89 C27 ca M 87 86 83 1.399 118.241 -178.023 -0.083
90 H ha E 89 87 86 1.090 119.773 -179.225 0.084
91 C28 ca M 89 87 86 1.403 120.871 -0.059 -0.083
92 H ha E 91 89 87 1.088 120.149 -179.992 0.084
93 C29 ca M 91 89 87 1.388 122.162 0.615 -0.077
94 H ha E 93 91 89 1.089 118.988 -179.808 0.085
95 C30 ca M 93 91 89 1.359 121.692 -0.439 -0.049
LOOP
N3 C2
C36 C32
C20 C15
C30 C22
C30 C25
IMPROPER
C2 N2 C3 O1
C31 C33 C32 C36
C32 H C33 N5
C35 H C34 N5
C34 C36 C35 H
C32 C35 C36 H
C14 C16 C15 C20
C15 C17 C16 H
C16 C18 C17 H
C17 C19 C18 H
C18 C20 C19 H
C15 C19 C20 H
C13 N4 C21 O3
C24 C26 C25 C30
C25 C27 C26 H
C26 C28 C27 H
C27 C29 C28 H
C28 C30 C29 H
C22 C25 C30 C29
DONE
STOP
Received on Thu Feb 20 2003 - 20:53:01 PST
