[gmx-users] Hem not found in residue topology database
Shumaila Khan
shumailakhan432 at yahoo.com
Thu Feb 9 08:14:18 CET 2017
Hello, Hopefully, You are all doing well. Version: 5.0.7 FF: 43a1 Spc watermodel
Heme topology is present in almost all the force fields. I want to simulate corn (Pdb id :2R50) containing heme. When I run simulation I get this error : "Residue HEM not found in residue topology database". As heme topology is available in rtp file then whats the reason I get this error.Following is my attached Hem structure.
HETATM 2341 FE HEM C1542 7.320 80.715 -5.955 1.00 25.63 FeHETATM 2342 CHA HEM C1542 7.828 77.591 -5.047 1.00 23.39 CHETATM 2343 CHB HEM C1542 6.501 81.578 -2.733 1.00 23.47 CHETATM 2344 CHC HEM C1542 6.798 84.039 -6.886 1.00 22.00 CHETATM 2345 CHD HEM C1542 7.415 79.872 -9.275 1.00 20.35 CHETATM 2346 NA HEM C1542 7.232 79.764 -4.194 1.00 25.04 NHETATM 2347 C1A HEM C1542 7.469 78.413 -3.980 1.00 25.77 CHETATM 2348 C2A HEM C1542 7.236 78.109 -2.602 1.00 26.75 CHETATM 2349 C3A HEM C1542 6.841 79.239 -1.971 1.00 26.16 CHETATM 2350 C4A HEM C1542 6.845 80.286 -2.956 1.00 24.77 CHETATM 2351 CMA HEM C1542 6.512 79.509 -0.487 1.00 23.24 CHETATM 2352 CAA HEM C1542 7.389 76.695 -1.990 1.00 30.57 CHETATM 2353 CBA HEM C1542 8.749 76.200 -1.503 1.00 34.82 CHETATM 2354 CGA HEM C1542 8.827 74.825 -0.843 1.00 37.87 CHETATM 2355 O1A HEM C1542 7.934 73.913 -0.680 1.00 39.74 OHETATM 2356 O2A HEM C1542 10.021 74.626 -0.423 1.00 40.42 OHETATM 2357 NB HEM C1542 6.751 82.455 -4.998 1.00 23.10 NHETATM 2358 C1B HEM C1542 6.460 82.611 -3.660 1.00 22.37 CHETATM 2359 C2B HEM C1542 6.131 83.997 -3.367 1.00 21.40 CHETATM 2360 C3B HEM C1542 6.235 84.681 -4.510 1.00 21.71 CHETATM 2361 C4B HEM C1542 6.614 83.714 -5.544 1.00 21.85 CHETATM 2362 CMB HEM C1542 5.830 84.540 -1.947 1.00 20.77 CHETATM 2363 CAB HEM C1542 6.009 86.177 -4.817 1.00 20.85 CHETATM 2364 CBB HEM C1542 4.894 86.822 -4.391 1.00 21.93 CHETATM 2365 NC HEM C1542 7.180 81.751 -7.717 1.00 23.07 NHETATM 2366 C1C HEM C1542 6.859 83.099 -7.910 1.00 21.16 CHETATM 2367 C2C HEM C1542 6.559 83.360 -9.301 1.00 19.55 CHETATM 2368 C3C HEM C1542 6.724 82.197 -9.967 1.00 19.24 CHETATM 2369 C4C HEM C1542 7.132 81.190 -9.023 1.00 21.12 CHETATM 2370 CMC HEM C1542 6.119 84.748 -9.815 1.00 17.45 CHETATM 2371 CAC HEM C1542 6.506 81.891 -11.455 1.00 17.62 CHETATM 2372 CBC HEM C1542 5.616 82.527 -12.236 1.00 18.11 CHETATM 2373 ND HEM C1542 7.593 79.010 -6.981 1.00 22.41 NHETATM 2374 C1D HEM C1542 7.635 78.876 -8.352 1.00 21.08 CHETATM 2375 C2D HEM C1542 7.835 77.476 -8.654 1.00 21.66 CHETATM 2376 C3D HEM C1542 7.913 76.830 -7.505 1.00 21.01 CHETATM 2377 C4D HEM C1542 7.763 77.760 -6.423 1.00 22.07 CHETATM 2378 CMD HEM C1542 7.919 76.887 -10.102 1.00 20.29 CHETATM 2379 CAD HEM C1542 8.131 75.321 -7.321 1.00 20.98 CHETATM 2380 CBD HEM C1542 6.723 74.752 -7.027 1.00 23.17 CHETATM 2381 CGD HEM C1542 6.768 73.298 -6.794 1.00 24.91 CHETATM 2382 O1D HEM C1542 6.242 72.753 -5.808 1.00 29.44 OHETATM 2383 O2D HEM C1542 7.406 72.657 -7.630 1.00 26.84 OHETATM 2384 HHA HEM C1542 8.236 76.638 -4.744 1.00 0.00 HHETATM 2385 HHB HEM C1542 6.228 81.833 -1.720 1.00 0.00 HHETATM 2386 HHC HEM C1542 6.899 85.082 -7.147 1.00 0.00 HHETATM 2387 HHD HEM C1542 7.471 79.584 -10.314 1.00 0.00 HHETATM 2388 HMA1 HEM C1542 5.559 79.043 -0.235 1.00 0.00 HHETATM 2389 HMA2 HEM C1542 7.298 79.091 0.141 1.00 0.00 HHETATM 2390 HMA3 HEM C1542 6.446 80.584 -0.319 1.00 0.00 HHETATM 2391 HAA2 HEM C1542 7.055 75.989 -2.750 1.00 0.00 HHETATM 2392 HAA3 HEM C1542 6.696 76.625 -1.151 1.00 0.00 HHETATM 2393 HBA2 HEM C1542 9.413 76.181 -2.367 1.00 0.00 HHETATM 2394 HBA3 HEM C1542 9.139 76.933 -0.797 1.00 0.00 HHETATM 2395 HMB1 HEM C1542 6.754 84.582 -1.370 1.00 0.00 HHETATM 2396 HMB2 HEM C1542 5.404 85.541 -2.024 1.00 0.00 HHETATM 2397 HMB3 HEM C1542 5.120 83.880 -1.449 1.00 0.00 HHETATM 2398 HAB HEM C1542 6.752 86.720 -5.381 1.00 0.00 HHETATM 2399 HBB1 HEM C1542 4.144 86.288 -3.826 1.00 0.00 HHETATM 2400 HBB2 HEM C1542 4.756 87.869 -4.617 1.00 0.00 HHETATM 2401 HMC1 HEM C1542 6.821 85.505 -9.465 1.00 0.00 HHETATM 2402 HMC2 HEM C1542 6.103 84.743 -10.905 1.00 0.00 HHETATM 2403 HMC3 HEM C1542 5.122 84.976 -9.438 1.00 0.00 HHETATM 2404 HAC HEM C1542 7.107 81.114 -11.904 1.00 0.00 HHETATM 2405 HBC1 HEM C1542 4.997 83.310 -11.823 1.00 0.00 HHETATM 2406 HBC2 HEM C1542 5.520 82.255 -13.277 1.00 0.00 HHETATM 2407 HMD1 HEM C1542 8.317 75.873 -10.060 1.00 0.00 HHETATM 2408 HMD2 HEM C1542 6.923 76.868 -10.545 1.00 0.00 HHETATM 2409 HMD3 HEM C1542 8.575 77.510 -10.710 1.00 0.00 HHETATM 2410 HAD2 HEM C1542 8.542 74.879 -8.229 1.00 0.00 HHETATM 2411 HAD3 HEM C1542 8.796 75.136 -6.477 1.00 0.00 HHETATM 2412 HBD2 HEM C1542 6.074 74.954 -7.879 1.00 0.00 HHETATM 2413 HBD3 HEM C1542 6.316 75.243 -6.143 1.00 0.00 HHETATM 2414 O1 OXY C1543 5.525 80.353 -6.212 1.00 25.38 OHETATM 2415 O2 OXY C1543 4.301 80.342 -6.721 1.00 30.35 OEND
Thanks in Advance
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