[gmx-users] Any ideas: Fatal error: Atom O in residue HEM XXX was not found in rtp entry while sorting atoms.
Matthew Fisher
matthew.fisher at stcatz.ox.ac.uk
Tue Nov 20 22:48:25 CET 2018
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.
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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