[gmx-users] Topology error
Justin Lemkul
jalemkul at vt.edu
Sun Feb 5 01:15:03 CET 2017
On 2/4/17 1:03 AM, Mehreen Jan wrote:
> Hello, I want to simulate heme of hemoglobin.I am using Gromacs version
> 5.0.7. and force feild GROMOS 96 43a1 and spc water model.I built Heme
> topology on Prodrg and Swiss param but Prodrg doesnt accept heme while Swiss
> param give errors. Kindly tell me appropriate force feild which I should use
> and How to generate iron and oxygen topology? or any alternative which I
> should use.Heme topology is available in almost all force feilds but It is
> for FE2+ not for FE3+ and I want to simulate FE3+. If it is possible, kindly
> please generate topology for heme containing oxygen. I shall be really very
> thankful to you.
>
You should not need external servers to generate a heme topology; GROMOS already
supports it. It's called HEME and it's in the .rtp file. Connections to
ligating residues should be recognized via existing entries in specbond.dat.
It seems that multiple people are asking the same question, so hopefully
everyone interested sees this post to avoid repetition.
-Justin
> This is the ligand , the heme atom.
>
> 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
>
> With best regards Mehreen Jan
>
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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