Open joaomcteixeira opened 2 years ago
However, when I rename the atoms HN
to H
It fails with the following:
Now working on 1110a_111.pdb
WARNING! These atoms are missing from the current backbone structure [1110a_111.pdb]:
1 H1
1 H2
1 H3
111 OXT
Start preparing energy calculators at different sidechain completion levels
Traceback (most recent call last):
File "/home/joao/anaconda3/envs/mcsce/bin/mcsce", line 33, in <module>
sys.exit(load_entry_point('mcsce', 'console_scripts', 'mcsce')())
File "/home/joao/github/MCSCE/src/mcsce/cli.py", line 36, in maincli
cli(parser, main)
File "/home/joao/github/MCSCE/src/mcsce/cli.py", line 31, in cli
main(**vars(cmd))
File "/home/joao/github/MCSCE/src/mcsce/cli.py", line 142, in main
forcefield=ff_obj, terms=["lj", "clash"]), structure=s)
File "/home/joao/github/MCSCE/src/mcsce/core/side_chain_builder.py", line 77, in initialize_func_calc
structure.res_labels))
File "/home/joao/github/MCSCE/src/mcsce/libs/libenergy.py", line 83, in prepare_energy_function
base_bool=False,
File "/home/joao/github/MCSCE/src/mcsce/libs/libenergy.py", line 324, in create_bonds_apart_mask_for_ij_pairs
if j_atom_name in bonds_intra[res_label][i_atom_name]:
KeyError: 'H'
I am pasting here the PDB, just 10 residues is enough to reproduce the error. Do you think MCSCE can be more versatile on this matter? Think that PDBs will have millions of forms :-x
ATOM 3 N MET 1 -39.879 34.489 108.809 N
ATOM 4 CA MET 1 -39.751 34.162 107.398 C
ATOM 5 C MET 1 -38.320 34.441 106.951 C
ATOM 6 O MET 1 -37.601 35.249 107.556 O
ATOM 7 CB MET 1 -40.710 35.030 106.571 C
ATOM 8 H MET 1 -39.314 35.243 109.200 H
ATOM 9 HA MET 1 -39.978 33.088 107.235 H
ATOM 10 N VAL 2 -37.887 33.772 105.882 N
ATOM 11 CA VAL 2 -36.540 33.956 105.365 C
ATOM 12 C VAL 2 -36.596 34.016 103.843 C
ATOM 13 O VAL 2 -37.179 33.143 103.183 O
ATOM 14 CB VAL 2 -35.652 32.778 105.787 C
ATOM 15 H VAL 2 -38.515 33.116 105.415 H
ATOM 16 HA VAL 2 -36.115 34.907 105.749 H
ATOM 17 N ARG 3 -35.987 35.051 103.263 N
ATOM 18 CA ARG 3 -35.976 35.212 101.817 C
ATOM 19 C ARG 3 -34.657 34.678 101.269 C
ATOM 20 O ARG 3 -34.479 34.523 100.051 O
ATOM 21 CB ARG 3 -36.102 36.697 101.454 C
ATOM 22 H ARG 3 -35.520 35.746 103.845 H
ATOM 23 HA ARG 3 -36.812 34.639 101.365 H
ATOM 24 N THR 4 -33.711 34.390 102.164 N
ATOM 25 CA THR 4 -32.413 33.874 101.757 C
ATOM 26 C THR 4 -32.115 32.603 102.544 C
ATOM 27 O THR 4 -32.578 32.423 103.680 O
ATOM 28 CB THR 4 -31.322 34.912 102.052 C
ATOM 29 H THR 4 -33.901 34.534 103.156 H
ATOM 30 HA THR 4 -32.424 33.634 100.673 H
ATOM 31 N LYS 5 -31.333 31.701 101.948 N
ATOM 32 CA LYS 5 -30.982 30.451 102.603 C
ATOM 33 C LYS 5 -29.533 30.526 103.073 C
ATOM 34 O LYS 5 -29.048 29.658 103.813 O
ATOM 35 CB LYS 5 -31.127 29.284 101.617 C
ATOM 36 H LYS 5 -30.974 31.891 101.012 H
ATOM 37 HA LYS 5 -31.639 30.286 103.483 H
ATOM 38 N ALA 6 -28.821 31.571 102.647 N
ATOM 39 CA ALA 6 -27.429 31.747 103.031 C
ATOM 40 C ALA 6 -27.320 32.947 103.965 C
ATOM 41 O ALA 6 -27.693 34.076 103.612 O
ATOM 42 CB ALA 6 -26.571 32.004 101.785 C
ATOM 43 H ALA 6 -29.262 32.261 102.039 H
ATOM 44 HA ALA 6 -27.065 30.842 103.561 H
ATOM 45 N GLU 7 -26.805 32.719 105.174 N
ATOM 46 CA GLU 7 -26.653 33.788 106.149 C
ATOM 47 C GLU 7 -25.189 34.209 106.198 C
ATOM 48 O GLU 7 -24.335 33.512 106.766 O
ATOM 49 CB GLU 7 -27.078 33.294 107.538 C
ATOM 50 H GLU 7 -26.512 31.773 105.421 H
ATOM 51 HA GLU 7 -27.271 34.661 105.852 H
ATOM 52 N SER 8 -24.878 35.361 105.601 N
ATOM 53 CA SER 8 -23.513 35.863 105.585 C
ATOM 54 C SER 8 -23.136 36.323 106.989 C
ATOM 55 O SER 8 -23.886 37.057 107.650 O
ATOM 56 CB SER 8 -23.405 37.053 104.623 C
ATOM 57 H SER 8 -25.613 35.901 105.146 H
ATOM 58 HA SER 8 -22.817 35.057 105.270 H
ATOM 59 N ILE 9 -21.966 35.896 107.464 N
ATOM 60 CA ILE 9 -21.503 36.271 108.791 C
ATOM 61 C ILE 9 -20.801 37.622 108.708 C
ATOM 62 O ILE 9 -20.469 38.112 107.619 O
ATOM 63 CB ILE 9 -20.511 35.224 109.315 C
ATOM 64 H ILE 9 -21.382 35.293 106.884 H
ATOM 65 HA ILE 9 -22.366 36.354 109.484 H
ATOM 66 N PRO 10 -20.566 38.245 109.864 N
ATOM 67 CA PRO 10 -19.902 39.539 109.908 C
ATOM 68 C PRO 10 -18.449 39.366 109.481 C
ATOM 69 O PRO 10 -17.778 40.326 109.072 O
ATOM 70 CB PRO 10 -19.940 40.098 111.336 C
ATOM 71 H PRO 10 -20.857 37.804 110.737 H
ATOM 72 HA PRO 10 -20.403 40.244 109.212 H
ATOM 73 N GLY 11 -17.942 38.136 109.569 N
ATOM 74 CA GLY 11 -16.567 37.853 109.190 C
ATOM 75 C GLY 11 -16.469 37.816 107.668 C
ATOM 76 O GLY 11 -15.444 38.186 107.078 O
ATOM 77 HA1 GLY 11 -16.139 36.490 109.751 H
ATOM 78 H GLY 11 -18.532 37.377 109.911 H
ATOM 79 HA2 GLY 11 -15.896 38.648 109.576 H
ATOM 80 N THR 12 -17.540 37.367 107.012 N
ATOM 81 CA THR 12 -17.561 37.287 105.560 C
ATOM 82 C THR 12 -17.986 38.638 104.995 C
ATOM 83 O THR 12 -18.641 39.444 105.672 O
ATOM 84 CB THR 12 -18.565 36.218 105.109 C
ATOM 85 H THR 12 -18.362 37.072 107.539 H
ATOM 86 HA THR 12 -16.548 37.039 105.179 H
ATOM 87 N LYS 13 -17.619 38.903 103.740 N
ATOM 88 CA LYS 13 -17.968 40.160 103.097 C
ATOM 89 C LYS 13 -18.669 39.864 101.776 C
ATOM 90 O LYS 13 -18.106 40.059 100.688 O
ATOM 91 CB LYS 13 -16.699 40.976 102.818 C
ATOM 92 H LYS 13 -17.081 38.210 103.220 H
ATOM 93 HA LYS 13 -18.655 40.741 103.748 H
In this case the issue is that the proline residue does not have amide proton, but the input structure has amide hydrogen for proline (residue 10), so MCSCE does not know what force field parameter to use for that atom. Maybe I should also provide a warning/error message in the beginning.
As for the HN atom name, it is not a standard in PDB format and therefore there is no corresponding records in the force field parameter file either. I think the users should modify the atom names, and I can provide a clearer error message for this as well.
I have a PDB that has
HN
instead ofH
for the amine protons. It fails when getting the data from the forcefield.gets the error:
Do you think it is possible to add an option also for these atoms, for example repeating the info, or is it best the user modifies the atom name beforehand?