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 Thu May 12 2016 - 11:00:04 PDT
