Thank you David for the clarification.
Just wondering where the old HEM parametrization files are located? It
seems they are removed from the current version i.e., 16.
Sincerely,
Morteza
2016-05-12 11:53 GMT-06:00 Morteza Chehel Amirani <morteza.amirani.gmail.com
>:
> Hi
>
> I have a problem in preparing the topology file for heme. It seems there
> were several posts on heme parameterization, but I still have problems. I
> have the resp charges for the following protonated heme with the net charge
> of +1 (iron is iron III in my case).
>
> I'm wondering if anyone could help me to construct the mol2 and frcmod
> files. It seems gaff recognizes the iron as "f" which is not correct.
>
> HETATM 1 FE HEM A 1 -12.834 66.481 35.483 1.00 20.00
> FE
> HETATM 2 CHA HEM A 1 -9.313 66.967 35.207 1.00 14.63
> C
> HETATM 3 CHB HEM A 1 -13.434 69.605 34.358 1.00 16.64
> C
> HETATM 4 CHC HEM A 1 -16.263 65.881 35.493 1.00 15.71
> C
> HETATM 5 CHD HEM A 1 -12.261 63.259 36.240 1.00 14.24
> C
> HETATM 6 NA HEM A 1 -11.667 67.890 34.859 1.00 16.85
> N
> HETATM 7 C1A HEM A 1 -10.198 67.940 34.796 1.00 16.94
> C
> HETATM 8 C2A HEM A 1 -9.730 69.209 34.379 1.00 17.80
> C
> HETATM 9 C3A HEM A 1 -10.876 69.917 34.114 1.00 17.33
> C
> HETATM 10 C4A HEM A 1 -12.076 69.122 34.445 1.00 17.28
> C
> HETATM 11 CMA HEM A 1 -10.990 71.313 33.521 1.00 15.69
> C
> HETATM 12 CAA HEM A 1 -8.287 69.639 34.237 1.00 19.21
> C
> HETATM 13 CBA HEM A 1 -7.874 69.738 32.785 1.00 19.23
> C
> HETATM 14 CGA HEM A 1 -6.452 70.217 32.607 1.00 23.40
> C
> HETATM 15 O1A HEM A 1 -5.868 69.903 31.567 1.00 27.60
> O
> HETATM 16 O2A HEM A 1 -5.896 70.921 33.468 1.00 22.89
> O
> HETATM 17 NB HEM A 1 -14.496 67.556 35.043 1.00 18.06
> N
> HETATM 18 C1B HEM A 1 -14.567 68.870 34.617 1.00 15.87
> C
> HETATM 19 C2B HEM A 1 -15.907 69.338 34.550 1.00 15.59
> C
> HETATM 20 C3B HEM A 1 -16.743 68.308 34.950 1.00 16.85
> C
> HETATM 21 C4B HEM A 1 -15.847 67.176 35.199 1.00 17.45
> C
> HETATM 22 CMB HEM A 1 -16.353 70.746 34.186 1.00 14.03
> C
> HETATM 23 CAB HEM A 1 -18.151 68.374 35.115 1.00 15.21
> C
> HETATM 24 CBB HEM A 1 -18.947 67.743 36.163 1.00 13.68
> C
> HETATM 25 NC HEM A 1 -14.035 64.940 35.729 1.00 14.93
> N
> HETATM 26 C1C HEM A 1 -15.423 64.835 35.668 1.00 13.97
> C
> HETATM 27 C2C HEM A 1 -15.861 63.453 35.753 1.00 13.45
> C
> HETATM 28 C3C HEM A 1 -14.730 62.684 35.941 1.00 13.90
> C
> HETATM 29 C4C HEM A 1 -13.614 63.621 35.961 1.00 14.85
> C
> HETATM 30 CMC HEM A 1 -17.329 62.986 35.790 1.00 13.05
> C
> HETATM 31 CAC HEM A 1 -14.561 61.291 36.073 1.00 12.51
> C
> HETATM 32 CBC HEM A 1 -15.358 60.306 36.828 1.00 11.73
> C
> HETATM 33 ND HEM A 1 -11.159 65.411 35.754 1.00 14.85
> N
> HETATM 34 C1D HEM A 1 -11.114 64.097 36.187 1.00 14.55
> C
> HETATM 35 C2D HEM A 1 -9.759 63.691 36.576 1.00 12.92
> C
> HETATM 36 C3D HEM A 1 -8.969 64.739 36.224 1.00 13.07
> C
> HETATM 37 C4D HEM A 1 -9.807 65.784 35.707 1.00 13.94
> C
> HETATM 38 CMD HEM A 1 -9.399 62.416 37.336 1.00 11.63
> C
> HETATM 39 CAD HEM A 1 -7.460 64.869 36.324 1.00 13.82
> C
> HETATM 40 CBD HEM A 1 -6.864 64.264 35.076 1.00 16.85
> C
> HETATM 41 CGD HEM A 1 -5.344 64.292 35.046 1.00 17.77
> C
> HETATM 42 O1D HEM A 1 -4.790 63.959 33.998 1.00 17.95
> O
> HETATM 43 O2D HEM A 1 -4.689 64.648 36.042 1.00 18.81
> O
> HETATM 44 HMA1 HEM A 1 -10.132 71.911 33.830 1.00 15.69
> H
> HETATM 45 HMA2 HEM A 1 -11.907 71.785 33.874 1.00 15.69
> H
> HETATM 46 HMA3 HEM A 1 -11.012 71.246 32.433 1.00 15.69
> H
> HETATM 47 HMB1 HEM A 1 -17.332 70.706 33.708 1.00 14.03
> H
> HETATM 48 HMB2 HEM A 1 -15.632 71.190 33.499 1.00 14.03
> H
> HETATM 49 HMB3 HEM A 1 -16.415 71.353 35.089 1.00 14.03
> H
> HETATM 50 HMC1 HEM A 1 -17.408 61.999 35.335 1.00 13.05
> H
> HETATM 51 HMC2 HEM A 1 -17.949 63.692 35.237 1.00 13.05
> H
> HETATM 52 HMC3 HEM A 1 -17.669 62.937 36.824 1.00 13.05
> H
> HETATM 53 HMD1 HEM A 1 -10.226 62.136 37.988 1.00 11.63
> H
> HETATM 54 HMD2 HEM A 1 -8.506 62.590 37.937 1.00 11.63
> H
> HETATM 55 HMD3 HEM A 1 -9.208 61.611 36.626 1.00 11.63
> H
> HETATM 56 HBB1 HEM A 1 -20.029 67.872 36.178 1.00 13.68
> H
> HETATM 57 HBB2 HEM A 1 -18.459 67.143 36.931 1.00 13.68
> H
> HETATM 58 HBC1 HEM A 1 -15.076 59.253 36.817 1.00 11.73
> H
> HETATM 59 HBC2 HEM A 1 -16.229 60.631 37.397 1.00 11.73
> H
> HETATM 60 HBA1 HEM A 1 -8.549 70.419 32.267 1.00 19.23
> H
> HETATM 61 HBA2 HEM A 1 -7.984 68.761 32.314 1.00 19.23
> H
> HETATM 62 HAA1 HEM A 1 -7.642 68.926 34.751 1.00 19.21
> H
> HETATM 63 HAA2 HEM A 1 -8.145 70.605 34.722 1.00 19.21
> H
> HETATM 64 HBD1 HEM A 1 -7.245 64.799 34.206 1.00 16.85
> H
> HETATM 65 HBD2 HEM A 1 -7.201 63.231 34.988 1.00 16.85
> H
> HETATM 66 HAD1 HEM A 1 -7.090 64.356 37.212 1.00 13.82
> H
> HETATM 67 HAD2 HEM A 1 -7.172 65.916 36.417 1.00 13.82
> H
> HETATM 68 HHA HEM A 1 -8.248 67.130 35.138 1.00 14.63
> H
> HETATM 69 HHB HEM A 1 -13.572 70.635 34.063 1.00 16.64
> H
> HETATM 70 HHC HEM A 1 -17.323 65.699 35.587 1.00 15.71
> H
> HETATM 71 HHD HEM A 1 -12.090 62.231 36.524 1.00 14.24
> H
> HETATM 72 HAB HEM A 1 -18.698 68.961 34.377 1.00 15.21
> H
> HETATM 73 HAC HEM A 1 -13.709 60.877 35.533 1.00 12.51
> H
> HETATM 74 HH1 HEM A 1 -5.355 71.859 33.500 1.00 0.00
> H
> HETATM 75 HH2 HEM A 1 -3.948 64.931 36.564 1.00 0.00
> H
> END
>
>
> Sincerely,
> Morteza
>
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Received on Fri May 13 2016 - 16:00:03 PDT
