ligand conformer generation for enzyme design

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    • February 12, 2013 at 12:51 am #1513
      Anonymous

        Hi everyone,
        I’m trying to generate ligand conformers for redesigning an enzyme. I had an input conformation, but when using it to generate conformers, it gave me this error:

        Loading internal fraglib
        81736 fragments loaded in 0.65 seconds

        Title = untitled
        Can’t assign MMFF type to atom number 44 S
        Warning: force field setup failed due to missing parameters for molecule untitled

        Can you give me some hints on solving this problem?
        Thanks.

      • February 12, 2013 at 1:55 am #8398
        Anonymous

          I’m going to guess the ligand automagic-machinery can’t figure out…something…about a sulfur atom. What is the chemical entity at that sulfur (thioether, thioester)? Does it look like any of the sulfur types in rosetta_database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt? (I think that’s the relevant file but I’m not sure).

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