a question about protein-ligand docking in generating 1SW2 conformers

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    • #1899

        Hii everyone,

        I am looking forward in prepareing 1SW2 ligand structures using rosettaligand arls package. I don’t generate ligand conformers in this case,

        Traceback (most recent call last):
        File “/home/ryhon/rosetta3.4/rosetta_source/src/python/apps/public/molfile_to_params.py”, line 1365, in
        File “/home/ryhon/rosetta3.4/rosetta_source/src/python/apps/public/molfile_to_params.py”, line 1284, in main
        molfiles = list(read_tripos_mol2(infile, do_find_rings=False))
        File “/home/ryhon/rosetta3.4/rosetta_source/src/python/rosetta_py/io/mdl_molfile.py”, line 421, in read_tripos_mol2
        else: raise ValueError(“no entries in MOL2 file”)
        ValueError: no entries in MOL2 file

        the omega2 log is :

        Running as Single Processor

        Title = 1SW2_A_L.pdb
        Warning: force field setup failed due to missing parameters for molecule 1SW2_A_L.pdb

        Number of Molecules Processed = 1
        Number of Molecules Failed = 1
        Elapsed time (s) = 2.3

        Omega job complete

        I don’t know how to resolve this problem. Please accept my sincere appreciation for you any help.

        thank u

      • #10073

          Ryhon Wang P-L Docking Question

        • #10075

            What’s your arls setup file look like? To work appropriately, you need to have the ligand you’re docking and the protein you’re docking specified in seperate files.

            Furthermore, the ligand needs to be in mol/sdf or mol2 file format — just PDB format won’t work. To convert from a PDB to a mol/sdf or mol2 file you need to use some structure editing program, like OpenBabel or Avogadro (or MOE or Sybyl, or …). Don’t forget to add hydrogens to your ligand prior to saving your ligand as a mol/sdf or mol2 format.

            From what I can tell you haven’t separated out the protein and ligand and/or haven’t converted the ligand to a mol/sdf or mol2 format.

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