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Error in for NCAA

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Error in for NCAA


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

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/", line 1995, in <module>
  File "/opt/rosetta_src_2020.11.61179_bundle/main/demos/public/design_with_ncaa/scripts/python/apps/public/", 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/", 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/", 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/", 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 to write the parameter files for diaminobutyric acid, homoserine, and tBu-Glycine. 

Post Situation: 
Mon, 2020-05-18 16:41

Those guys are definitely in the database. See for their names.

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

Sat, 2020-05-23 03:09