Hi
i think a +1 charge should be not correct, iron has mainly +2 or +3
oxidation state.
Probably antechamber with bcc does not work well with metals.
Inside the amber distributions there are some heme parameters:
/Users/Jacopo/amber11/dat/contrib/heme
try to use them. Maybe you can use the heme.lib from the amber
distribution and calculate more appropriate atomic charges using
gaussian and the resp fitting.
jacopo
2011/4/8 Indrek Morell <indrekm80.hot.ee>:
> 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 - 11:00:04 PDT
