Hi,
I'm trying to create lib for custom molecule - heme, which has to propionate groups
unprotonated (-2 charge) and iron atom at the centre. There should probably be +1 charge on Fe
atom (four coordinative bonds)
Input line:
./antechamber -i
$AmberRun/NewMol/HEM.pdb -fi pdb -o $AmberRun/NewMol/HEM.mol2 -fo mol2 -c bcc -s 2 -nc
-1
But alas, something is not right and i get an error message with
antechamber:
Total number of electrons: 308; net charge: -1
Running:
/home/indrek/amber11/bin/sqm -O -i sqm.in -o sqm.out
Error: cannot run
"/home/indrek/amber11/bin/sqm -O -i sqm.in -o sqm.out" of bcc() in charge.c properly,
exit
Maybe it has something to do with spin multiplicity but i' m not sure...
Any
ideas? PDB file at the end of message
Thanks in
advance,
Indrek
HETATM 1 CAA HEM B
601 70.270 38.347 172.380 1.00
33.17 C
HETATM 2 CAA HEM B 601 70.771
35.803 173.047 1.00 28.68
C
HETATM 3 CAB HEM B 601
74.779 29.897 169.662 1.00
25.49 C
HETATM 4 CAB HEM B 601 73.135
33.097 170.710 1.00 24.64
C
HETATM 5 CAC HEM B 601
71.299 28.418 176.829 1.00
26.50 C
HETATM 6 CAC HEM B 601 72.499
30.022 173.657 1.00 25.41
C
HETATM 7 CAD HEM B 601
68.244 35.884 176.734 1.00
23.47 C
HETATM 8 CAD HEM B 601 70.097
32.719 175.963 1.00 25.57
C
HETATM 9 CAE HEM B 601
70.891 36.960 172.166 1.00
30.36 C
HETATM
10 CAF HEM B 601 73.919 32.350 169.750 1.00
24.50 C
HETATM
11 CAG HEM B 601 72.385 28.860 174.538 1.00
25.89 C
HETATM
12 CAH HEM B 601 69.207 33.459 176.846 1.00
25.02 C
HETATM
13 CAI HEM B 601 71.660 36.557 171.122 1.00
29.10 C
HETATM
14 CAJ HEM B 601 74.040 31.084 170.302 1.00
24.16 C
HETATM
15 CAK HEM B 601 71.624 29.257 175.582 1.00
25.74 C
HETATM
16 CAL HEM B 601 69.088 34.693 176.266 1.00
25.63 C
HETATM
17 CAM HEM B 601 72.015 35.174 171.373 1.00
27.55 C
HETATM
18 CAN HEM B 601 73.323 31.104 171.586 1.00
24.46 C
HETATM
19 CAO HEM B 601 71.267 30.653 175.340 1.00
25.08 C
HETATM
20 CAP HEM B 601 69.903 34.683 175.075 1.00
26.32 C
HETATM
21 NA HEM B 601 71.479 34.721 172.563 1.00
28.01 N
HETATM
22 CBA HEM B 601 71.466 39.260 172.719 1.00
38.39 C
HETATM
23 CBB HEM B 601 76.241 30.156 169.302 1.00
26.79 C
HETATM
24 CBC HEM B 601 69.849 28.086 177.128 1.00
26.49 C
HETATM
25 CBD HEM B 601 66.803 35.755 176.219 1.00
22.99 C
HETATM
26 NB HEM B 601 72.760 32.353 171.831 1.00
24.45 N
HETATM
27 ND HEM B 601 70.508 33.467 174.878 1.00
25.82 N
HETATM
28 CHA HEM B 601 70.041 35.775 174.215 1.00
27.71 C
HETATM
29 CHB HEM B 601 72.777 34.416 170.528 1.00
26.03 C
HETATM
30 CHC HEM B 601 73.199 30.024 172.454 1.00
25.11 C
HETATM
31 CHD HEM B 601 70.467 31.412 176.175 1.00
25.28 C
HETATM
32 CMA HEM B 601 72.072 37.406 169.906 1.00
27.30 C
HETATM
33 CMB HEM B 601 74.472 32.889 168.401 1.00
21.72 C
HETATM
34 CMC HEM B 601 73.019 27.476 174.289 1.00
26.10 C
HETATM
35 CMD HEM B 601 68.543 32.938 178.133 1.00
25.18 C
HETATM
36 O01 HEM B 601 66.631 38.022 177.005 1.00
24.20 O
HETATM
37 O02 HEM B 601 64.709 36.698 176.930 1.00
24.20 O
HETATM
38 O03 HEM B 601 69.931 40.874 173.624 1.00
41.74 O
HETATM
39 O04 HEM B 601 72.225 41.260 173.819 1.00
41.74 O
HETATM
40 C11 HEM B 601 71.198 40.728 172.978 1.00
41.74 C
HETATM
41 C12 HEM B 601 65.944 37.001 176.276 1.00
24.20 C
HETATM
42 NC HEM B 601 71.820 31.119 174.162 1.00
25.45 N
HETATM
43 FE HEM B 601 71.677 32.942 173.362 1.00
24.09 FE
HETATM
44 H01 HEM B 601 68.493 33.742 178.868 1.00
25.18 H
HETATM
45 H02 HEM B 601 69.555 38.327 173.202 1.00
33.17 H
HETATM
46 H03 HEM B 601 74.250 29.623 168.749 1.00
25.49 H
HETATM
47 H04 HEM B 601 71.689 28.959 177.691 1.00
26.50 H
HETATM
48 H05 HEM B 601 68.681 36.807 176.352 1.00
23.47 H
HETATM
49 H06 HEM B 601 72.164 39.201 171.884 1.00
38.39 H
HETATM
50 H07 HEM B 601 76.541 31.133 169.681 1.00
26.79 H
HETATM
51 H08 HEM B 601 69.533 28.614 178.028 1.00
26.49 H
HETATM
52 H09 HEM B 601 66.308 34.985 176.811 1.00
22.99 H
HETATM
53 H10 HEM B 601 69.522 36.692 174.495 1.00
27.71 H
HETATM
54 H11 HEM B 601 73.137 34.902 169.621 1.00
26.03 H
HETATM
55 H12 HEM B 601 73.694 29.097 172.166 1.00
25.11 H
HETATM
56 H13 HEM B 601 70.097 30.932 177.081 1.00
25.28 H
HETATM
57 H14 HEM B 601 72.009 38.464 170.163 1.00
27.30 H
HETATM
58 H15 HEM B 601 74.466 33.979 168.415 1.00
21.72 H
HETATM
59 H16 HEM B 601 73.148 27.322 173.218 1.00
26.10 H
HETATM
60 H17 HEM B 601 69.129 32.112 178.536 1.00
25.18 H
HETATM
61 H18 HEM B 601 69.721 38.693 171.505 1.00
33.17 H
HETATM
62 H19 HEM B 601 74.789 29.108 170.414 1.00
25.49 H
HETATM
63 H20 HEM B 601 71.754 27.449 176.621 1.00
26.50 H
HETATM
64 H21 HEM B 601 68.229 35.900 177.824 1.00
23.47 H
HETATM
65 H22 HEM B 601 71.831 38.881 173.674 1.00
38.39 H
HETATM
66 H23 HEM B 601 76.358 30.134 168.219 1.00
26.79 H
HETATM
67 H24 HEM B 601 69.746 27.012 177.281 1.00
26.49 H
HETATM
68 H25 HEM B 601 66.899 35.523 175.158 1.00
22.99 H
HETATM
69 H26 HEM B 601 71.404 37.194 169.071 1.00
27.30 H
HETATM
70 H27 HEM B 601 73.847 32.532 167.583 1.00
21.72 H
HETATM
71 H28 HEM B 601 72.369 26.700 174.693 1.00
26.10 H
HETATM
72 H29 HEM B 601 67.535 32.591 177.906 1.00
25.18 H
HETATM
73 H30 HEM B 601 76.867 29.385 169.751 1.00
26.79 H
HETATM
74 H31 HEM B 601 69.226 28.395 176.289 1.00
26.49 H
HETATM
75 H32 HEM B 601 73.096 37.161 169.623 1.00
27.30 H
HETATM
76 H33 HEM B 601 75.493 32.534 168.259 1.00
21.72 H
HETATM
77 H34 HEM B 601 73.990 27.428 174.782 1.00
26.10 H
END
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Received on Fri Apr 08 2011 - 10:00:04 PDT
