Error in molfile_to_params_polymer.py for NCAA

[Anonymous]

Hello,

I have been following this tutorial but have been getting an error at step 5.

https://www.rosettacommons.org/demos/latest/public/using_ncaas_protein_peptide_interface_design/README

I am trying to convert the NCAA, ornithine, in the demo from the modifiled mol file to a parameter file. However, I consistently receive this error message. I am concerned because the modifiled mol file from the demo is already in the V2000 version of the mol file. 

Traceback (most recent call last):

  File “/opt/rosetta_src_2020.11.61179_bundle/main/demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py”, line 1995, in <module>

    sys.exit(main(sys.argv[1:]))

  File “/opt/rosetta_src_2020.11.61179_bundle/main/demos/public/design_with_ncaa/scripts/python/apps/public/molfile_to_params_polymer.py”, line 1915, in main

    molfiles = read_mdl_sdf(infile)

  File “/opt/rosetta_src_2020.11.61179_bundle/main/demos/public/design_with_ncaa/scripts/python/rosetta_py/io/mdl_molfile.py”, line 271, in read_mdl_sdf

    ret = read_mdl_sdf(f, do_find_rings)

  File “/opt/rosetta_src_2020.11.61179_bundle/main/demos/public/design_with_ncaa/scripts/python/rosetta_py/io/mdl_molfile.py”, line 276, in read_mdl_sdf

    molfile = read_mdl_molfile(f, do_find_rings)

  File “/opt/rosetta_src_2020.11.61179_bundle/main/demos/public/design_with_ncaa/scripts/python/rosetta_py/io/mdl_molfile.py”, line 201, in read_mdl_molfile

    raise ValueError(“can only read V2000 format files”)

 

Any advice or guidance would be greatly appreciated. I would like to use molfile_to_params_polymer.py to write the parameter files for diaminobutyric acid, homoserine, and tBu-Glycine. 

[Anonymous]

Those guys are definitely in the database. See https://github.com/matteoferla/Display-of-preset-Rosetta-NCAAs for their names.

That is you will find the topology file in database > chemical > residues > full atom > nncaa or something like that.

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