Problem passing a list of PDB files to minimize_with_cst

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    • November 19, 2018 at 12:13 am #3039
      Anonymous

        Hello

        I am trying to minimze a structure using the minimize_with_cst script.

        However, I keep getting the error message:

        ERROR: Cannot open file “ATOM”

        Based on this thread , I thoghout that I should use the in:file:s option instead of in:file:l which is recoomende in the ddg_monomer documenation, but I still get this error.

        The error presist wheter I pass the list of pdbs as a variable, or pass a file that containts the names of the PDB files (as suggetsed here) but I invaribly get this error.

        The command that I am passing is: 


        
/path/to/minimize_with_cst.linuxgccrelease -in:file:l $pdbs_to_minimize <I also tried this with -in:file:s>  -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database $ROSETTA_DB -ddg::harmonic_ca_tether 0.5 - -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false -beta_nov15 > mincst.log

        Where the content of $pdbs_to_minmize is:

        S_0025.pdb S_0948.pdb S_0728.pdb S_0564.pdb S_0484.pdb

         

        Any  help will be apprecaited

         

        Dolev

      • November 21, 2018 at 11:31 pm #14503
        Anonymous

          The -l option of Rosetta expects a filename of a text file which lists the PDBs to be used, one per line. It shouldn’t be used with a list of PDB files on the commandline. (Hence the error – Rosetta is opening the PDB, then treating the ATOM in the file as the name of a PDB it is supposed to open.)

           

          You’re right that the -s option should work with a list of PDBs on the commandline. However minimize_with_cst has a bug in that it treats -s like -l. That bug has now been fixed, but it may be a bit before the next weekly release is released.

          Until then, print the list of PDBs into a file, and then pass that filename to the -l option.

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