[gmx-users] Topology error

Sotirios Dionysios I. Papadatos si.papadatos at edu.cut.ac.cy
Sun Feb 5 17:13:28 CET 2017


Furthermore external servers fail to parameterize Fe, so it is of no use anyway. You should find the missing parameters in the literature.

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Justin Lemkul <jalemkul at vt.edu>
Sent: Sunday, February 5, 2017 2:14:51 AM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Topology error



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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