I am trying to define a new residue to AMBER forcefield in gromacs. pdb2gmx is giving "missing atoms" error (All atoms are reported as missing) when I define all the hydrogens in the .rtp file under the residue. If however, I do not define all hydrogens but some of them, the pdb2gmx reports the missing hydrogens instead and recognizes the atoms. I can create the topology with -ignh argument. I've also added hydrogen definitions to the corresponding .hdb file, it still gives the same error.
Please provide the exact error message, the contents of your .rtp entry, and the relevant snippet of your input coordinate file.
Hi, @Justin Lemkul
Thank you for your interest. I am just trying to create a topology without giving any charge to the molecule. Given below is the error message and the corresponding .rtp entry
WARNING: atom O12 is missing in residue UNK 1 in the pdb file
^"This warning is written for all atoms"
Fatal error:
There were 175 missing atoms in molecule Protein, if you want to use this incomplete topology anyhow, use the option -missing
Resides in the .rtp
[ LIG ]; Rod
[ atoms ]
C1 C 0 0
C2 C 0 0
C3 C 0 0
C4 C 0 0
C5 C 0 0
C6 C 0 6
C7 C 0 7
C8 C 0 8
C9 C 0 9
C10 C 0 10
C11 C 0 11
C12 C 0 12
C13 C 0 13
C14 C 0 14
C15 C 0 15
C16 C 0 16
C17 C 0 17
C18 C 0 18
C19 C 0 19
C20 C 0 20
C21 C 0 21
C22 C 0 22
C23 C 0 23
C24 C 0 24
C25 C 0 25
N1 N 0 38
N2 N 0 39
N3 N 0 40
N4 N 0 41
N5 N 0 42
N6 N 0 43
N7 N 0 44
H1 HC 0 75
H2 HC 0 76
H3 HC 0 77
H4 HC 0 78
H5 HC 0 79
H6 HC 0 80
H7 HC 0 81
H8 HC 0 82
H9 HC 0 83
H10 HC 0 84
H11 HC 0 85
H12 HC 0 86
H13 HC 0 87
H14 HC 0 88
H15 HC 0 89
H16 HC 0 90
H17 HC 0 91
H18 HC 0 92
H19 HC 0 93
H20 HC 0 94
H21 HC 0 95
H22 HC 0 96
H23 HC 0 97
H24 HC 0 98
H25 HC 0 99
H26 HC 0 100
H27 HC 0 101
H28 HC 0 102
H29 HC 0 103
H30 HC 0 104
H31 HC 0 105
H32 HC 0 106
H33 HC 0 106
[ UNK ]
[ atoms ]
C1 C 0 1
C3 C 0 3
C4 C 0 4
C5 C 0 5
C6 C 0 6
C7 C 0 7
C8 C 0 8
C9 C 0 9
C10 C 0 10
C11 C 0 11
C12 C 0 12
C13 C 0 13
C14 C 0 14
C15 C 0 15
C16 C 0 16
C17 C 0 17
C18 C 0 18
C19 C 0 19
C20 C 0 20
C21 C 0 21
C22 C 0 22
C23 C 0 23
C24 C 0 24
C25 C 0 25
C26 C 0 26
C27 C 0 27
C28 C 0 28
C29 C 0 29
C30 C 0 30
C31 C 0 31
C32 C 0 32
C33 C 0 33
C34 C 0 34
C35 C 0 35
C36 C 0 36
C37 C 0 37
N1 N 0 38
N2 N 0 39
N3 N 0 40
N4 N 0 41
N5 N 0 42
N6 N 0 43
N7 N 0 44
N8 N 0 45
N9 N 0 46
N10 N 0 47
N11 N 0 48
N12 N 0 49
N13 N 0 50
N14 N 0 51
N15 N 0 52
N16 N 0 53
N17 N 0 54
N18 N 0 55
N19 N 0 56
N20 N 0 57
N21 N 0 58
N22 N 0 59
N23 N 0 60
N24 N 0 61
O1 O 0 62
O2 O 0 63
O3 O 0 64
O4 O 0 65
O5 O 0 66
O6 O 0 67
O7 O 0 68
O8 O 0 69
O9 O 0 70
O10 O 0 71
O11 O 0 72
O12 O 0 73
H1 HC 0 75
H2 HC 0 76
H3 HC 0 77
H4 HC 0 78
H5 HC 0 79
H6 HC 0 80
H7 HC 0 81
H8 HC 0 82
H9 HC 0 83
H10 HC 0 84
H11 HC 0 85
H12 HC 0 86
H13 HC 0 87
H14 HC 0 88
H15 HC 0 89
H16 HC 0 90
H17 HC 0 91
H18 HC 0 92
H19 HC 0 93
H20 HC 0 94
H21 HC 0 95
H22 HC 0 96
H23 HC 0 97
H24 HC 0 98
H25 HC 0 99
H26 HC 0 100
H27 HC 0 101
H28 HC 0 102
H29 HC 0 103
H30 HC 0 104
H31 HC 0 105
H32 HC 0 106
H33 HC 0 107
H34 HC 0 108
H35 HC 0 109
H36 HC 0 110
H37 HC 0 110
A section from the corresponding pdb file;
ATOM 11 C9 LIG 1 -2.837 -5.166 -10.076 1.00 0.00 C
ATOM 12 C10 LIG 1 -2.081 -3.874 -9.879 1.00 0.00 C
ATOM 13 C11 LIG 1 -0.674 -3.845 -9.828 1.00 0.00 C
ATOM 14 C12 LIG 1 0.009 -2.642 -9.633 1.00 0.00 C
ATOM 15 C13 LIG 1 -0.694 -1.432 -9.500 1.00 0.00 C
ATOM 16 C14 LIG 1 -2.088 -1.455 -9.554 1.00 0.00 C
ATOM 17 C15 LIG 1 -2.777 -2.657 -9.744 1.00 0.00 C
ATOM 18 C16 LIG 1 0.057 -0.143 -9.239 1.00 0.00 C
ATOM 19 N3 LIG 1 0.153 0.788 -10.389 1.00 0.00 N
ATOM 20 C17 LIG 1 -1.022 1.640 -10.600 1.00 0.00 C
ATOM 21 C18 LIG 1 -0.737 2.702 -11.635 1.00 0.00 C
ATOM 22 C19 LIG 1 -0.697 4.059 -11.426 1.00 0.00 C
ATOM 23 N4 LIG 1 -0.426 4.632 -12.613 1.00 0.00 N
ATOM 24 N5 LIG 1 -0.306 3.669 -13.511 1.00 0.00 N
ATOM 25 N6 LIG 1 -0.483 2.481 -12.940 1.00 0.00 N
ATOM 26 C20 LIG 1 -0.313 6.080 -12.848 1.00 0.00 C
ATOM 27 C21 LIG 1 -0.209 6.553 -14.310 1.00 0.00 C
ATOM 28 N7 LIG 1 1.068 6.189 -14.944 1.00 0.00 N
ATOM 29 C22 LIG 1 1.330 6.802 -16.280 1.00 0.00 C
ATOM 30 C23 LIG 1 2.630 6.190 -16.849 1.00 0.00 C
ATOM 31 C24 LIG 1 0.185 6.519 -17.281 1.00 0.00 C
ATOM 32 C25 LIG 1 1.537 8.332 -16.167 1.00 0.00 C
ATOM 33 O1 UNK 1 2.224 1.372 -7.837 1.00 0.00 O
ATOM 34 C1 UNK 1 2.709 2.416 -8.241 1.00 0.00 C
ATOM 35 N1 UNK 1 3.676 2.469 -9.173 1.00 0.00 N
ATOM 36 N2 UNK 1 2.346 3.619 -7.770 1.00 0.00 N
ATOM 37 C3 UNK 1 4.326 1.288 -9.744 1.00 0.00 C
ATOM 38 C4 UNK 1 3.195 4.648 -8.322 1.00 0.00 C
ATOM 39 O2 UNK 1 2.651 -0.768 -10.757 1.00 0.00 O
ATOM 40 C5 UNK 1 3.178 0.011 -11.534 1.00 0.00 C
ATOM 41 N3 UNK 1 3.050 -0.087 -12.868 1.00 0.00 N
ATOM 42 N4 UNK 1 3.960 1.030 -11.136 1.00 0.00 N
ATOM 43 C6 UNK 1 2.298 -1.142 -13.542 1.00 0.00 C
ATOM 44 C7 UNK 1 4.554 1.665 -12.292 1.00 0.00 C
ATOM 45 O3 UNK 1 -0.373 -1.560 -12.665 1.00 0.00 O
ATOM 46 C8 UNK 1 -0.170 -0.962 -13.712 1.00 0.00 C
ATOM 47 N5 UNK 1 -1.158 -0.598 -14.549 1.00 0.00 N
ATOM 48 N6 UNK 1 1.063 -0.667 -14.166 1.00 0.00 N
ATOM 49 C9 UNK 1 -2.547 -0.999 -14.389 1.00 0.00 C
ATOM 50 C10 UNK 1 0.967 -0.139 -15.512 1.00 0.00 C
ATOM 51 O4 UNK 1 2.667 6.201 -11.355 1.00 0.00 O
ATOM 52 C11 UNK 1 2.969 5.446 -10.445 1.00 0.00 C
ATOM 53 N7 UNK 1 3.838 4.433 -10.595 1.00 0.00 N
ATOM 54 N8 UNK 1 2.511 5.586 -9.188 1.00 0.00 N
ATOM 55 C12 UNK 1 4.592 4.184 -11.809 1.00 0.00 C
ATOM 56 C13 UNK 1 4.133 3.836 -9.316 1.00 0.00 C
ATOM 57 O5 UNK 1 3.053 4.133 -14.170 1.00 0.00 O
ATOM 58 C14 UNK 1 3.422 3.082 -13.675 1.00 0.00 C
ATOM 59 N9 UNK 1 3.236 1.889 -14.262 1.00 0.00 N
ATOM 60 N10 UNK 1 4.106 3.017 -12.524 1.00 0.00 N
ATOM 61 C15 UNK 1 2.736 1.724 -15.619 1.00 0.00 C
ATOM 62 C16 UNK 1 3.925 0.866 -13.515 1.00 0.00 C
ATOM 63 O6 UNK 1 0.397 3.189 -16.233 1.00 0.00 O
ATOM 64 C17 UNK 1 0.311 2.000 -15.974 1.00 0.00 C
ATOM 65 N11 UNK 1 -0.848 1.328 -15.993 1.00 0.00 N
ATOM 66 N12 UNK 1 1.367 1.243 -15.645 1.00 0.00 N
ATOM 67 C18 UNK 1 1.389 3.820 -6.698 1.00 0.00 C
ATOM 68 C19 UNK 1 -0.600 -0.082 -15.774 1.00 0.00 C
ATOM 69 N13 UNK 1 -3.391 0.094 -13.936 1.00 0.00 N
ATOM 70 C20 UNK 1 1.723 6.731 -8.731 1.00 0.00 C
ATOM 71 C21 UNK 1 -2.124 1.923 -16.371 1.00 0.00 C
ATOM 72 N14 UNK 1 0.126 4.357 -7.182 1.00 0.00 N
ATOM 73 C22 UNK 1 -3.972 1.111 -14.784 1.00 0.00 C
ATOM 74 C23 UNK 1 -3.890 0.191 -12.698 1.00 0.00 C
ATOM 75 N15 UNK 1 0.323 6.405 -8.475 1.00 0.00 N
ATOM 76 N16 UNK 1 -3.028 2.104 -15.238 1.00 0.00 N
ATOM 77 C24 UNK 1 -1.002 3.636 -7.272 1.00 0.00 C
ATOM 78 C25 UNK 1 -0.184 5.764 -7.280 1.00 0.00 C
ATOM 79 C26 UNK 1 -4.906 1.922 -13.786 1.00 0.00 C
ATOM 80 O7 UNK 1 -3.632 -0.605 -11.812 1.00 0.00 O
ATOM 81 N17 UNK 1 -4.709 1.237 -12.527 1.00 0.00 N
ATOM 82 C27 UNK 1 -0.702 6.829 -9.236 1.00 0.00 C
ATOM 83 C28 UNK 1 -3.334 3.300 -14.700 1.00 0.00 C
ATOM 84 O8 UNK 1 -1.039 2.427 -7.093 1.00 0.00 O
ATOM 85 N18 UNK 1 -2.095 4.375 -7.519 1.00 0.00 N
ATOM 86 C29 UNK 1 -1.758 5.779 -7.505 1.00 0.00 C
ATOM 87 N19 UNK 1 -4.354 3.257 -13.822 1.00 0.00 N
ATOM 88 C30 UNK 1 -5.437 1.506 -11.299 1.00 0.00 C
ATOM 89 O9 UNK 1 -0.551 7.505 -10.241 1.00 0.00 O
ATOM 90 N20 UNK 1 -1.910 6.447 -8.782 1.00 0.00 N
ATOM 91 O10 UNK 1 -2.777 4.339 -15.023 1.00 0.00 O
ATOM 92 C31 UNK 1 -3.447 3.854 -7.482 1.00 0.00 C
ATOM 93 C32 UNK 1 -5.022 4.442 -13.288 1.00 0.00 C
ATOM 94 N21 UNK 1 -4.904 2.649 -10.572 1.00 0.00 N
ATOM 95 C33 UNK 1 -3.180 6.853 -9.388 1.00 0.00 C
ATOM 96 N22 UNK 1 -4.013 3.723 -8.811 1.00 0.00 N
ATOM 97 N23 UNK 1 -4.717 4.686 -11.884 1.00 0.00 N
ATOM 98 C34 UNK 1 -5.334 4.015 -10.761 1.00 0.00 C
ATOM 99 C35 UNK 1 -4.210 2.549 -9.427 1.00 0.00 C
ATOM 100 N24 UNK 1 -3.861 5.775 -10.107 1.00 0.00 N
ATOM 101 C36 UNK 1 -4.717 4.773 -9.508 1.00 0.00 C
ATOM 102 C37 UNK 1 -3.967 5.710 -11.447 1.00 0.00 C
ATOM 103 O11 UNK 1 -3.839 1.483 -8.962 1.00 0.00 O
ATOM 104 O12 UNK 1 -3.460 6.525 -12.198 1.00 0.00 O
HETATM 105 H1 LIG 1 -0.715 -8.081 -7.258 1.00 0.00 H
HETATM 106 H2 LIG 1 -0.808 -5.646 -8.066 1.00 0.00 H
HETATM 107 H3 LIG 1 -3.774 -7.804 -10.166 1.00 0.00 H
HETATM 108 H4 LIG 1 -3.093 -8.983 -7.994 1.00 0.00 H
HETATM 109 H5 LIG 1 -1.976 -9.394 -9.206 1.00 0.00 H
HETATM 110 H6 LIG 1 -3.787 -3.238 -12.125 1.00 0.00 H
Make sure each residue has a different residue number and that each is contiguous (you have LIG split, and everything has a residue number of 1). Also note that atom names O1 and O2 will be translated to different names per xlateat.dat - the error message says you're trying to define these residues (or some others) as Protein, which will trigger the use of xlateat.dat renaming.
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