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