adding greek_alphabets in non-canonical AA parameter generation

[Anonymous]

Hello

I am running molfile_to_params_polymer.py to get the .params file for my non-canonical aa. But I got the error below. I think it might be due to the long chain of my non-canonical amino acid. I tried to increase the greek letters list in line 1655 of the script, but it did not work. Maybe it needs to modiy several lines of code.

Also, I got large numbers (as you see the error below).Can someone help to modify the code for my non-canonical  amino acid to resolve the error?

I am attaching my molfile, pdb file of my non-canonical AA and rhe modified script of  molfile_to_params_polymer.py as well.

Thanks

 

( H56  H   -2.056   10.494    1.504) [1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 31, 1e+100, 1e+100, 30, 28, 15, 22, 29, 26, 18, 25, 25, 24, 26, 20, 26, 15, 24, 29, 23, 27, 21, 29, 20, 19, 17, 16, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 0, 1e+100, 1e+100, 1e+100]

( H57  H   -0.785    9.479    2.160) [1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 31, 1e+100, 1e+100, 30, 28, 15, 22, 29, 26, 18, 25, 25, 24, 26, 20, 26, 15, 24, 29, 23, 27, 21, 29, 20, 19, 17, 16, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 0, 1e+100, 1e+100]

( H58  H   -0.737    9.965    0.475) [1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 31, 1e+100, 1e+100, 30, 28, 15, 22, 29, 26, 18, 25, 25, 24, 26, 20, 26, 15, 24, 29, 23, 27, 21, 29, 20, 19, 17, 16, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 0, 1e+100]

( H59  H    5.873    1.241   -1.550) [1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 5, 1e+100, 1e+100, 4, 2, 15, 8, 3, 4, 12, 7, 5, 8, 6, 12, 6, 17, 6, 3, 7, 3, 9, 1, 10, 11, 13, 14, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 0]

ALL TO ALL DIST CA INDEX

[1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 0, 1e+100, 1e+100, 1, 3, 16, 9, 2, 5, 13, 8, 6, 9, 7, 13, 7, 18, 7, 4, 8, 4, 10, 4, 11, 12, 14, 15, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100, 1e+100]

Traceback (most recent call last):

  File “molfile_to_params_polymer.py”, line 1995, in <module>

    sys.exit(main(sys.argv[1:]))

  File “molfile_to_params_polymer.py”, line 1953, in main

    polymer_assign_pdb_like_atom_names_to_sidechain( m.atoms, m.bonds, options.peptoid )

  File “molfile_to_params_polymer.py”, line 1697, in polymer_assign_pdb_like_atom_names_to_sidechain

    a.pdb_greek_dist = greek_alphabet[all_all_dist[ca_index]]

IndexError: list index out of range

 

[Anonymous]

I would just use molfile_to_params for that — it should be classified as a ligand by Rosetta, not as a polymeric type.

[Anonymous]

Thanks for the response.

Does it make sense that non-canonical residue classidied as a ligand by Rosetta? If I use molfile_to_param.py, I need to modify that file to convert it to polymer, right?

Also, since I followed working with Non-canonical residue steps in the paper below, my noncanonical residue has acetylated-N terminus and N-methylated C-terminus. Therefore, the parameter file generated by molfile_to_param.py does not have the upper and lower lines. Is it   fine I add them manually and remove acetylated-N terminus and N-methylated C-terminus?

[Author]

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