[gmx-users] Any ideas: Fatal error: Atom O in residue HEM XXX was not found in rtp entry while sorting atoms.

Justin Lemkul jalemkul at vt.edu
Wed Nov 21 00:29:40 CET 2018



On 11/20/18 4:48 PM, Matthew Fisher wrote:
> Dear all,
>
>
> I wonder if anyone could offer some advice on a current issue I've got. I'm currently trying to simulate a Heme protein using GROMACS and the AMBER99SB-ildn force field. Parametisation for this system has been done previously for AMBER (
>
> https://doi.org/10.1002/jcc.21922
> ) and through consulting the manual and a handy tutorial off the mailing list (https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2015-September/101115.html) , I've been able to adapt the parameters into the GROMACS force field. The protein is a 458 aa polypeptide with a heme group ligated via a Fe-S bond to a CYS at position 400.
>
>
> My issue is, when running pdb2gmx (gmx pdb2gmx -f XXX1.pdb -o cyp.gro -merge all), I get this output:
>
> Atom O in residue HEM 471 was not found in rtp entry HEME with 74 atoms
> while sorting atoms.
>
> Only problem is, I've accounted for all the oxygen atoms in the rtp/pdb files, so I'm a little stuck as to what the problem is? Does anyone have any ideas at this stage; it would be greatly appreciated? Similar work has been done in the literature so I know this simulation is possible in GROMACS.

GROMACS is interpreting the atom O1 as a C-terminal carboxyl oxygen atom 
(O1 and O2 are translated to O and OXT). The conversion is specified in 
xlateat.dat in $GMXLIB. The simplest fix is to not use the atom name O1 
in your custom residue.

-Justin

> Thanks,
> Matt
>
> [ HEME ]
>   [ atoms ]
>      NC   ncr  -0.0333    1
>     C1C    ccr          -0.0836     2
>     C4C    ccr          -0.0148     3
>     C2C    ccr          -0.0025     4
>     C3C    ccr          -0.1636     5
>     CHD    cgr           0.0470     6
>     HHD    har           0.0773     7
>     C1D    cdr          -0.1256     8
>      ND    ndr           0.0685     9
>     C4D    cdr          -0.0340    10
>     C3D    cdr          -0.0325    11
>     C2D    cdr           0.0288    12
>     CHA    cgr          -0.0124    13
>     HHA    har           0.1920    14
>     C1A    ccr          -0.0365    15
>     C2A    ccr          -0.0626    16
>     C4A    ccr          -0.0543    17
>      NA    ncr          -0.0015    18
>     C3A    ccr           0.0097    19
>     CHB    cgr           0.0210    20
>     HHB    har           0.1004    21
>     C1B    cdr          -0.1156    22
>     C2B    cdr           0.0805    23
>      NB    ndr           0.0339    24
>     C4B    cdr          -0.0866    25
>     CHC    cgr           0.0569    26
>     HHC    har           0.0740    27
>      FE    fer           0.2620    28
>     C3B    cdr          -0.0237    29
>     CAB    ccr          -0.0963    30
>     HAB    har           0.1169    31
>     CBB    cdr          -0.3967    32
>    HBB1    har           0.1410    33
>    HBB2    har           0.1410    34
>     CAC    cdr           0.0915    35
>     HAC    har           0.0767    36
>     CBC    ccr          -0.4715    37
>    HBC1    har           0.1517    38
>    HBC2    har           0.1517    39
>     CMB    c3r          -0.1258    40
>    HMB1    hcr           0.0397    41
>    HMB2    hcr           0.0397    42
>    HMB3    hcr           0.0397    43
>     CMC    c3r           0.0353    44
>    HMC1    hcr           0.0049    45
>    HMC2    hcr           0.0049    46
>    HMC3    hcr           0.0049    47
>     CMD    c3r          -0.2123    48
>    HMD1    hcr           0.0653    49
>    HMD2    hcr           0.0653    50
>    HMD3    hcr           0.0653    51
>     CMA    c3r          -0.0747    52
>    HMA1    hcr           0.0306    53
>    HMA2    hcr           0.0306    54
>    HMA3    hcr           0.0306    55
>     CAA    c3r          -0.0115    56
>    HAA1    hcr           0.0253    57
>    HAA2    hcr           0.0253    58
>     CAD    c3r          -0.0659    59
>    HAD1    hcr           0.0364    60
>    HAD2    hcr           0.0364    61
>     CBA    c3r          -0.0304    62
>    HBA1    h1r          -0.0023    63
>    HBA2    h1r          -0.0023    64
>     CBD    c3r          -0.0022    65
>    HBD1    h1r           0.0140    66
>    HBD2    h1r           0.0140    67
>     CGD    cr            0.5749    68
>     CGA    cr            0.6402    69
>     O1A    or           -0.6508    70
>     O1D    or           -0.6552    71
>     O2A    or           -0.6508    72
>     O2D    or           -0.6552    73
>      O1    oar          -0.3729    74
>
> PDB extract
>
> TER    3758      ILE B 458
> HETATM 3759  CAA HEM B 471       1.755  18.131 -15.889  1.00 15.51           C
> HETATM 3760  CAB HEM B 471      -4.791  24.485 -11.701  1.00 20.40           C
> HETATM 3761  CAC HEM B 471       2.533  27.567 -10.509  1.00 18.35           C
> HETATM 3762  CAD HEM B 471       5.798  21.469 -14.505  1.00 17.29           C
> HETATM 3763  NA  HEM B 471       0.386  21.111 -13.959  1.00 17.77           N
> HETATM 3764  CBA HEM B 471       1.855  18.352 -17.427  1.00 19.79           C
> HETATM 3765  CBB HEM B 471      -5.966  23.773 -11.004  1.00 26.67           C
> HETATM 3766  CBC HEM B 471       2.417  28.024  -9.048  1.00 27.22           C
> HETATM 3767  CBD HEM B 471       6.499  20.615 -13.335  1.00 17.56           C
> HETATM 3768  NB  HEM B 471      -1.463  22.941 -12.743  1.00 15.71           N
> HETATM 3769  CGA HEM B 471       2.524  17.345 -18.205  1.00 19.93           C
> HETATM 3770  CGD HEM B 471       7.641  19.908 -13.762  1.00 20.58           C
> HETATM 3771  ND  HEM B 471       2.513  22.853 -13.219  1.00 16.35           N
> HETATM 3772  CHA HEM B 471       2.762  20.715 -14.442  1.00 17.63           C
> HETATM 3773  CHB HEM B 471      -2.057  20.891 -14.014  1.00 20.44           C
> HETATM 3774  CHC HEM B 471      -1.724  25.024 -11.443  1.00 17.83           C
> HETATM 3775  CHD HEM B 471       3.065  25.025 -12.165  1.00 21.60           C
> HETATM 3776  CMA HEM B 471      -1.524  18.310 -15.643  1.00 17.42           C
> HETATM 3777  CMB HEM B 471      -4.986  21.674 -13.454  1.00 20.09           C
> HETATM 3778  CMC HEM B 471      -0.770  27.534  -9.911  1.00 19.11           C
> HETATM 3779  CMD HEM B 471       5.977  24.412 -13.134  1.00 20.15           C
> HETATM 3780  C1A HEM B 471       1.411  20.355 -14.511  1.00 18.03           C
> HETATM 3781  C1B HEM B 471      -2.388  22.049 -13.283  1.00 19.13           C
> HETATM 3782  C1C HEM B 471      -0.394  25.357 -11.365  1.00 17.65           C
> HETATM 3783  C1D HEM B 471       3.413  23.851 -12.875  1.00 19.45           C
> HETATM 3784  O1A HEM B 471       2.810  16.231 -17.621  1.00 19.81           O
> HETATM 3785  O1D HEM B 471       8.744  20.054 -13.132  1.00 19.49           O
> HETATM 3786  C2A HEM B 471       0.897  19.181 -15.185  1.00 15.87           C
> HETATM 3787  C2B HEM B 471      -3.762  22.449 -12.993  1.00 18.51           C
> HETATM 3788  C2C HEM B 471       0.116  26.541 -10.688  1.00 18.38           C
> HETATM 3789  C2D HEM B 471       4.769  23.528 -13.327  1.00 17.19           C
> HETATM 3790  O2A HEM B 471       2.839  17.520 -19.393  1.00 18.08           O
> HETATM 3791  O2D HEM B 471       7.599  19.160 -14.777  1.00 19.41           O
> HETATM 3792  C3A HEM B 471      -0.473  19.243 -15.090  1.00 17.13           C
> HETATM 3793  C3B HEM B 471      -3.680  23.608 -12.262  1.00 19.05           C
> HETATM 3794  C3C HEM B 471       1.466  26.538 -10.935  1.00 18.71           C
> HETATM 3795  C3D HEM B 471       4.689  22.315 -13.902  1.00 16.11           C
> HETATM 3796  C4A HEM B 471      -0.773  20.456 -14.321  1.00 19.43           C
> HETATM 3797  C4B HEM B 471      -2.244  23.906 -12.120  1.00 19.13           C
> HETATM 3798  C4C HEM B 471       1.778  25.367 -11.707  1.00 19.27           C
> HETATM 3799  C4D HEM B 471       3.266  21.902 -13.868  1.00 19.57           C
> HETATM 3800  NC  HEM B 471       0.655  24.606 -11.941  1.00 17.74           N
> HETATM 3801  FE  HEM B 471       0.539  22.816 -12.859  1.00 18.57          Fe
> HETATM 3802  O1  HEM B 471       0.562  23.667 -14.260  1.00  0.00           O
>
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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