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starwingc / peptoid_24summer

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Having trouble with making a capping residue #5

Closed starwingc closed 4 months ago

starwingc commented 4 months ago

Trying to make a capping residues looks like this

path at :peptoid_24summer/peptoid/17AB1-5-A/CNNE

image

the mol2:

@<TRIPOS>MOLECULE
CNNE
31 32 1 0 0
SMALL
NO_CHARGES

@<TRIPOS>ATOM
      1 C1          4.4243   -0.4418    0.8602 C.3       1 NNE        0.0000
      2 C2          3.0564    0.1667    0.6883 C.2       1 NNE        0.0000
      3 O1          2.4410    0.5589    1.6570 O.2       1 NNE        0.0000
      4 N           2.5168    0.2749   -0.5420 N.am      1 NNE        0.0000
      5 C3          1.1870    0.8664   -0.7092 C.3       1 NNE        0.0000
      6 H1          1.0559    1.6750    0.0100 H         1 NNE        0.0000
      7 C4          1.0496    1.4196   -2.1290 C.3       1 NNE        0.0000
      8 C5          0.1354   -0.1878   -0.4768 C.ar      1 NNE        0.0000
      9 C6          0.4396   -1.5048   -0.6383 C.ar      1 NNE        0.0000
     10 C7         -0.5194   -2.4935   -0.4280 C.ar      1 NNE        0.0000
     11 C8         -1.7881   -2.1713   -0.0546 C.ar      1 NNE        0.0000
     12 C9         -2.1393   -0.8224    0.1223 C.ar      1 NNE        0.0000
     13 C10        -3.4391   -0.4509    0.5067 C.ar      1 NNE        0.0000
     14 C11        -3.7430    0.8658    0.6682 C.ar      1 NNE        0.0000
     15 C12        -2.7839    1.8549    0.4576 C.ar      1 NNE        0.0000
     16 C13        -1.5154    1.5328    0.0842 C.ar      1 NNE        0.0000
     17 C14        -1.1624    0.1832   -0.0868 C.ar      1 NNE        0.0000
     18 H2          4.6906   -0.4443    1.9171 H         1 NNE        0.0000
     19 H3          4.4165   -1.4652    0.4851 H         1 NNE        0.0000
     20 H4          5.1552    0.1439    0.3027 H         1 NNE        0.0000
     21 H5          3.0089   -0.0388   -1.3168 H         1 NNE        0.0000
     22 H6          1.1806    0.6110   -2.8482 H         1 NNE        0.0000
     23 H7          0.0602    1.8597   -2.2534 H         1 NNE        0.0000
     24 H8          1.8102    2.1821   -2.2971 H         1 NNE        0.0000
     25 H9          1.4390   -1.7875   -0.9342 H         1 NNE        0.0000
     26 H10        -0.2521   -3.5311   -0.5637 H         1 NNE        0.0000
     27 H11        -2.5211   -2.9484    0.1045 H         1 NNE        0.0000
     28 H12        -4.1929   -1.2063    0.6728 H         1 NNE        0.0000
     29 H13        -4.7426    1.1486    0.9636 H         1 NNE        0.0000
     30 H14        -3.0514    2.8925    0.5923 H         1 NNE        0.0000
     31 H15        -0.7829    2.3100   -0.0761 H         1 NNE        0.0000
@<TRIPOS>BOND
     1    1    2 1
     2    2    3 2
     3    2    4 am
     4    4    5 1
     5    5    6 1
     6    5    7 1
     7    5    8 1
     8    8    9 ar
     9    9   10 ar
    10   10   11 ar
    11   11   12 ar
    12   12   13 ar
    13   13   14 ar
    14   14   15 ar
    15   15   16 ar
    16   16   17 ar
    17   12   17 ar
    18    8   17 ar
    19    1   18 1
    20    1   19 1
    21    1   20 1
    22    4   21 1
    23    7   22 1
    24    7   23 1
    25    7   24 1
    26    9   25 1
    27   10   26 1
    28   11   27 1
    29   13   28 1
    30   14   29 1
    31   15   30 1
    32   16   31 1
@<TRIPOS>SUBSTRUCTURE
     1 NNE        1 RESIDUE           4 A     NNE     0 ROOT

the errors are:

>> parmchk2 -i NNE.edited.mol2 -f mol2 -o NNE.edited.mol2.frcmod -p $CONDA_PREFIX/dat/leap/parm/gaff.dat
Traceback (most recent call last):
  File "/Users/starwingchen/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py", line 341, in <module>
    leapscript += tleap_residue_lines(out_mol2, p.ResidueName, p.CNTerm, CappingAtoms, HeadAtom=p.HeadAtom, TailAtom=p.TailAtom)
  File "/Users/starwingchen/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py", line 143, in tleap_residue_lines
    leaptxt += 'set %s tail %s.1.%d\n'%(res,res,ResObject.get_atom_id_by_name(TailAtom))
TypeError: %d format: a number is required, not NoneType
starwingc commented 4 months ago

command is wrong... making a N terminal instead of desired C terminal instead :(