Re: [AMBER] Heme .lib file for heme - problem

From: Jacopo Sgrignani <sgrigna.sissa.it>
Date: Fri, 8 Apr 2011 19:51:18 +0200

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
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