[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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