[gmx-users] HEME issue
Mehreen Jan
mehreen_jan1990 at yahoo.com
Thu Feb 9 11:54:54 CET 2017
hello every one
i want to simulate HEME using gromacs 5.0.7 ff43A1 . i read some where HEME is already present in almost all gromacs FF. when i run Pdb2gmx.......HEME.gro i got error Residue 'HEM' not found in residue topology database. i compare my PDB with rtp file ... i am shocked to see that my PDB HEM and rtp [HEME] are completely different. i have no idea what to do and how to do??
i have no access to CHARMM-GUI, SwissParam give me error and ATB didnot provide login password. if some one have HEM modified topology kindly upload it or send.
my HEME:
HETATM 1 FE HEM C1542 7.320 80.715 -5.955 1.00 25.63 Fe
HETATM 2 CHA HEM C1542 7.828 77.591 -5.047 1.00 23.39 C
HETATM 3 CHB HEM C1542 6.501 81.578 -2.733 1.00 23.47 C
HETATM 4 CHC HEM C1542 6.798 84.039 -6.886 1.00 22.00 C
HETATM 5 CHD HEM C1542 7.415 79.872 -9.275 1.00 20.35 C
HETATM 6 NA HEM C1542 7.232 79.764 -4.194 1.00 25.04 N
HETATM 7 C1A HEM C1542 7.469 78.413 -3.980 1.00 25.77 C
HETATM 8 C2A HEM C1542 7.236 78.109 -2.602 1.00 26.75 C
HETATM 9 C3A HEM C1542 6.841 79.239 -1.971 1.00 26.16 C
HETATM 10 C4A HEM C1542 6.845 80.286 -2.956 1.00 24.77 C
HETATM 11 CMA HEM C1542 6.512 79.509 -0.487 1.00 23.24 C
HETATM 12 CAA HEM C1542 7.389 76.695 -1.990 1.00 30.57 C
HETATM 13 CBA HEM C1542 8.749 76.200 -1.503 1.00 34.82 C
HETATM 14 CGA HEM C1542 8.827 74.825 -0.843 1.00 37.87 C
HETATM 15 O1A HEM C1542 7.934 73.913 -0.680 1.00 39.74 O
HETATM 16 O2A HEM C1542 10.021 74.626 -0.423 1.00 40.42 O
HETATM 17 NB HEM C1542 6.751 82.455 -4.998 1.00 23.10 N
HETATM 18 C1B HEM C1542 6.460 82.611 -3.660 1.00 22.37 C
HETATM 19 C2B HEM C1542 6.131 83.997 -3.367 1.00 21.40 C
HETATM 20 C3B HEM C1542 6.235 84.681 -4.510 1.00 21.71 C
HETATM 21 C4B HEM C1542 6.614 83.714 -5.544 1.00 21.85 C
HETATM 22 CMB HEM C1542 5.830 84.540 -1.947 1.00 20.77 C
HETATM 23 CAB HEM C1542 6.009 86.177 -4.817 1.00 20.85 C
HETATM 24 CBB HEM C1542 4.894 86.822 -4.391 1.00 21.93 C
HETATM 25 NC HEM C1542 7.180 81.751 -7.717 1.00 23.07 N
HETATM 26 C1C HEM C1542 6.859 83.099 -7.910 1.00 21.16 C
HETATM 27 C2C HEM C1542 6.559 83.360 -9.301 1.00 19.55 C
HETATM 28 C3C HEM C1542 6.724 82.197 -9.967 1.00 19.24 C
HETATM 29 C4C HEM C1542 7.132 81.190 -9.023 1.00 21.12 C
HETATM 30 CMC HEM C1542 6.119 84.748 -9.815 1.00 17.45 C
HETATM 31 CAC HEM C1542 6.506 81.891 -11.455 1.00 17.62 C
HETATM 32 CBC HEM C1542 5.616 82.527 -12.236 1.00 18.11 C
HETATM 33 ND HEM C1542 7.593 79.010 -6.981 1.00 22.41 N
HETATM 34 C1D HEM C1542 7.635 78.876 -8.352 1.00 21.08 C
HETATM 35 C2D HEM C1542 7.835 77.476 -8.654 1.00 21.66 C
HETATM 36 C3D HEM C1542 7.913 76.830 -7.505 1.00 21.01 C
HETATM 37 C4D HEM C1542 7.763 77.760 -6.423 1.00 22.07 C
HETATM 38 CMD HEM C1542 7.919 76.887 -10.102 1.00 20.29 C
HETATM 39 CAD HEM C1542 8.131 75.321 -7.321 1.00 20.98 C
HETATM 40 CBD HEM C1542 6.723 74.752 -7.027 1.00 23.17 C
HETATM 41 CGD HEM C1542 6.768 73.298 -6.794 1.00 24.91 C
HETATM 42 O1D HEM C1542 6.242 72.753 -5.808 1.00 29.44 O
HETATM 43 O2D HEM C1542 7.406 72.657 -7.630 1.00 26.84 O
HETATM 44 HHA HEM C1542 8.236 76.638 -4.744 1.00 0.00 H
HETATM 45 HHB HEM C1542 6.228 81.833 -1.720 1.00 0.00 H
HETATM 46 HHC HEM C1542 6.899 85.082 -7.147 1.00 0.00 H
HETATM 47 HHD HEM C1542 7.471 79.584 -10.314 1.00 0.00 H
HETATM 48 HMA1 HEM C1542 5.559 79.043 -0.235 1.00 0.00 H
HETATM 49 HMA2 HEM C1542 7.298 79.091 0.141 1.00 0.00 H
HETATM 50 HMA3 HEM C1542 6.446 80.584 -0.319 1.00 0.00 H
HETATM 51 HAA2 HEM C1542 7.055 75.989 -2.750 1.00 0.00 H
HETATM 52 HAA3 HEM C1542 6.696 76.625 -1.151 1.00 0.00 H
HETATM 53 HBA2 HEM C1542 9.413 76.181 -2.367 1.00 0.00 H
HETATM 54 HBA3 HEM C1542 9.139 76.933 -0.797 1.00 0.00 H
HETATM 55 HMB1 HEM C1542 6.754 84.582 -1.370 1.00 0.00 H
HETATM 56 HMB2 HEM C1542 5.404 85.541 -2.024 1.00 0.00 H
HETATM 57 HMB3 HEM C1542 5.120 83.880 -1.449 1.00 0.00 H
HETATM 58 HAB HEM C1542 6.752 86.720 -5.381 1.00 0.00 H
HETATM 59 HBB1 HEM C1542 4.144 86.288 -3.826 1.00 0.00 H
HETATM 60 HBB2 HEM C1542 4.756 87.869 -4.617 1.00 0.00 H
HETATM 61 HMC1 HEM C1542 6.821 85.505 -9.465 1.00 0.00 H
HETATM 62 HMC2 HEM C1542 6.103 84.743 -10.905 1.00 0.00 H
HETATM 63 HMC3 HEM C1542 5.122 84.976 -9.438 1.00 0.00 H
HETATM 64 HAC HEM C1542 7.107 81.114 -11.904 1.00 0.00 H
HETATM 65 HBC1 HEM C1542 4.997 83.310 -11.823 1.00 0.00 H
HETATM 66 HBC2 HEM C1542 5.520 82.255 -13.277 1.00 0.00 H
HETATM 67 HMD1 HEM C1542 8.317 75.873 -10.060 1.00 0.00 H
HETATM 68 HMD2 HEM C1542 6.923 76.868 -10.545 1.00 0.00 H
HETATM 69 HMD3 HEM C1542 8.575 77.510 -10.710 1.00 0.00 H
HETATM 70 HAD2 HEM C1542 8.542 74.879 -8.229 1.00 0.00 H
HETATM 71 HAD3 HEM C1542 8.796 75.136 -6.477 1.00 0.00 H
HETATM 72 HBD2 HEM C1542 6.074 74.954 -7.879 1.00 0.00 H
HETATM 73 HBD3 HEM C1542 6.316 75.243 -6.143 1.00 0.00 H
END
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