[gmx-users] rtp is not compatable with heme
Mehreen Jan
mehreen_jan1990 at yahoo.com
Thu Feb 9 08:30:26 CET 2017
Hello, any one plz help
Version: 5.0.7
FF: 43a1
Heme topology is present in almost all the force fields. I want to simulate corn (Pdb id :IHHO) 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. i examine rtp file it is not compatible with my pdb both are different
Following is rtp fie of HEME this HEME is not compatible with my HEM i dont know whats the issue i even examine other PDBs containg HEM ...HEM are same in PDBs but not compatible with rtp file .
[ HEME ]
[ atoms ]
FE FE 0.40000 0
NA NR -0.10000 0
NB NR -0.10000 0
NC NR -0.10000 0
ND NR -0.10000 0
CHA C -0.10000 1
HHA HC 0.10000 1
C1A C 0.00000 2
C2A C 0.00000 2
C3A C 0.00000 2
C4A C 0.00000 2
CMA CH3 0.00000 3
CAA CH2 0.00000 4
CBA CH2 0.00000 4
CGA C 0.27000 5
O1A OM -0.63500 5
O2A OM -0.63500 5
CHB C -0.10000 6
HHB HC 0.10000 6
C1B C 0.00000 7
C2B C 0.00000 7
C3B C 0.00000 7
C4B C 0.00000 7
CMB CH3 0.00000 8
CAB CR1 0.00000 9
CBB CH2 0.00000 9
CHC C -0.10000 10
HHC HC 0.10000 10
C1C C 0.00000 11
C2C C 0.00000 11
C3C C 0.00000 11
C4C C 0.00000 11
CMC CH3 0.00000 12
CAC CR1 0.00000 13
CBC CH2 0.00000 13
CHD C -0.10000 14
HHD HC 0.10000 14
C1D C 0.00000 15
C2D C 0.00000 15
C3D C 0.00000 15
C4D C 0.00000 15
CMD CH3 0.00000 16
CAD CH2 0.00000 17
CBD CH2 0.00000 17
CGD C 0.27000 18
O1D OM -0.63500 18
O2D OM -0.63500 18
HEM of my PDB
HETATM 2341 FE HEM C1542 7.320 80.715 -5.955 1.00 25.63 Fe
HETATM 2342 CHA HEM C1542 7.828 77.591 -5.047 1.00 23.39 C
HETATM 2343 CHB HEM C1542 6.501 81.578 -2.733 1.00 23.47 C
HETATM 2344 CHC HEM C1542 6.798 84.039 -6.886 1.00 22.00 C
HETATM 2345 CHD HEM C1542 7.415 79.872 -9.275 1.00 20.35 C
HETATM 2346 NA HEM C1542 7.232 79.764 -4.194 1.00 25.04 N
HETATM 2347 C1A HEM C1542 7.469 78.413 -3.980 1.00 25.77 C
HETATM 2348 C2A HEM C1542 7.236 78.109 -2.602 1.00 26.75 C
HETATM 2349 C3A HEM C1542 6.841 79.239 -1.971 1.00 26.16 C
HETATM 2350 C4A HEM C1542 6.845 80.286 -2.956 1.00 24.77 C
HETATM 2351 CMA HEM C1542 6.512 79.509 -0.487 1.00 23.24 C
HETATM 2352 CAA HEM C1542 7.389 76.695 -1.990 1.00 30.57 C
HETATM 2353 CBA HEM C1542 8.749 76.200 -1.503 1.00 34.82 C
HETATM 2354 CGA HEM C1542 8.827 74.825 -0.843 1.00 37.87 C
HETATM 2355 O1A HEM C1542 7.934 73.913 -0.680 1.00 39.74 O
HETATM 2356 O2A HEM C1542 10.021 74.626 -0.423 1.00 40.42 O
HETATM 2357 NB HEM C1542 6.751 82.455 -4.998 1.00 23.10 N
HETATM 2358 C1B HEM C1542 6.460 82.611 -3.660 1.00 22.37 C
HETATM 2359 C2B HEM C1542 6.131 83.997 -3.367 1.00 21.40 C
HETATM 2360 C3B HEM C1542 6.235 84.681 -4.510 1.00 21.71 C
HETATM 2361 C4B HEM C1542 6.614 83.714 -5.544 1.00 21.85 C
HETATM 2362 CMB HEM C1542 5.830 84.540 -1.947 1.00 20.77 C
HETATM 2363 CAB HEM C1542 6.009 86.177 -4.817 1.00 20.85 C
HETATM 2364 CBB HEM C1542 4.894 86.822 -4.391 1.00 21.93 C
HETATM 2365 NC HEM C1542 7.180 81.751 -7.717 1.00 23.07 N
HETATM 2366 C1C HEM C1542 6.859 83.099 -7.910 1.00 21.16 C
HETATM 2367 C2C HEM C1542 6.559 83.360 -9.301 1.00 19.55 C
HETATM 2368 C3C HEM C1542 6.724 82.197 -9.967 1.00 19.24 C
HETATM 2369 C4C HEM C1542 7.132 81.190 -9.023 1.00 21.12 C
HETATM 2370 CMC HEM C1542 6.119 84.748 -9.815 1.00 17.45 C
HETATM 2371 CAC HEM C1542 6.506 81.891 -11.455 1.00 17.62 C
HETATM 2372 CBC HEM C1542 5.616 82.527 -12.236 1.00 18.11 C
HETATM 2373 ND HEM C1542 7.593 79.010 -6.981 1.00 22.41 N
HETATM 2374 C1D HEM C1542 7.635 78.876 -8.352 1.00 21.08 C
HETATM 2375 C2D HEM C1542 7.835 77.476 -8.654 1.00 21.66 C
HETATM 2376 C3D HEM C1542 7.913 76.830 -7.505 1.00 21.01 C
HETATM 2377 C4D HEM C1542 7.763 77.760 -6.423 1.00 22.07 C
HETATM 2378 CMD HEM C1542 7.919 76.887 -10.102 1.00 20.29 C
HETATM 2379 CAD HEM C1542 8.131 75.321 -7.321 1.00 20.98 C
HETATM 2380 CBD HEM C1542 6.723 74.752 -7.027 1.00 23.17 C
HETATM 2381 CGD HEM C1542 6.768 73.298 -6.794 1.00 24.91 C
HETATM 2382 O1D HEM C1542 6.242 72.753 -5.808 1.00 29.44 O
HETATM 2383 O2D HEM C1542 7.406 72.657 -7.630 1.00 26.84 O
HETATM 2384 HHA HEM C1542 8.236 76.638 -4.744 1.00 0.00 H
HETATM 2385 HHB HEM C1542 6.228 81.833 -1.720 1.00 0.00 H
HETATM 2386 HHC HEM C1542 6.899 85.082 -7.147 1.00 0.00 H
HETATM 2387 HHD HEM C1542 7.471 79.584 -10.314 1.00 0.00 H
HETATM 2388 HMA1 HEM C1542 5.559 79.043 -0.235 1.00 0.00 H
HETATM 2389 HMA2 HEM C1542 7.298 79.091 0.141 1.00 0.00 H
HETATM 2390 HMA3 HEM C1542 6.446 80.584 -0.319 1.00 0.00 H
HETATM 2391 HAA2 HEM C1542 7.055 75.989 -2.750 1.00 0.00 H
HETATM 2392 HAA3 HEM C1542 6.696 76.625 -1.151 1.00 0.00 H
HETATM 2393 HBA2 HEM C1542 9.413 76.181 -2.367 1.00 0.00 H
HETATM 2394 HBA3 HEM C1542 9.139 76.933 -0.797 1.00 0.00 H
HETATM 2395 HMB1 HEM C1542 6.754 84.582 -1.370 1.00 0.00 H
HETATM 2396 HMB2 HEM C1542 5.404 85.541 -2.024 1.00 0.00 H
HETATM 2397 HMB3 HEM C1542 5.120 83.880 -1.449 1.00 0.00 H
HETATM 2398 HAB HEM C1542 6.752 86.720 -5.381 1.00 0.00 H
HETATM 2399 HBB1 HEM C1542 4.144 86.288 -3.826 1.00 0.00 H
HETATM 2400 HBB2 HEM C1542 4.756 87.869 -4.617 1.00 0.00 H
HETATM 2401 HMC1 HEM C1542 6.821 85.505 -9.465 1.00 0.00 H
HETATM 2402 HMC2 HEM C1542 6.103 84.743 -10.905 1.00 0.00 H
HETATM 2403 HMC3 HEM C1542 5.122 84.976 -9.438 1.00 0.00 H
HETATM 2404 HAC HEM C1542 7.107 81.114 -11.904 1.00 0.00 H
HETATM 2405 HBC1 HEM C1542 4.997 83.310 -11.823 1.00 0.00 H
HETATM 2406 HBC2 HEM C1542 5.520 82.255 -13.277 1.00 0.00 H
HETATM 2407 HMD1 HEM C1542 8.317 75.873 -10.060 1.00 0.00 H
HETATM 2408 HMD2 HEM C1542 6.923 76.868 -10.545 1.00 0.00 H
HETATM 2409 HMD3 HEM C1542 8.575 77.510 -10.710 1.00 0.00 H
HETATM 2410 HAD2 HEM C1542 8.542 74.879 -8.229 1.00 0.00 H
HETATM 2411 HAD3 HEM C1542 8.796 75.136 -6.477 1.00 0.00 H
HETATM 2412 HBD2 HEM C1542 6.074 74.954 -7.879 1.00 0.00 H
HETATM 2413 HBD3 HEM C1542 6.316 75.243 -6.143 1.00 0.00 H
HETATM 2414 O1 OXY C1543 5.525 80.353 -6.212 1.00 25.38 O
HETATM 2415 O2 OXY C1543 4.301 80.342 -6.721 1.00 30.35 O
END
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