Reply To: some application troubles when using resfile flag

[Anonymous]

I don’t know where the syntax error is from. Here’s the contents of the help (from -h):

molfile_to_params.py -h
Usage: molfile_to_params.py [flags] { INPUT.mol | INPUT.sdf | INPUT.mol2 }

Converts a small molecule in an MDL Molfile with “M SPLT” and “M ROOT”
records into a series of .params residue definition files for Rosetta. Also
writes out the ligand conformation as PDB HETATMs. If an SD file is given as
input instead, the first entry is used for generating topology / parameter
files, and they all are used for generating PDB-style coordinates in separate,
numbered files. Multiple models may also be supplied in MOL2 format, which
does not support M ROOT and M SPLT records but does allow for partial charges.
File type is deduced from the extension. To divide a ligand into fragments by
“breaking” bonds (optional): M SPLT atom_no1 atom_no2 To specify a neighbor
atom for a ligand fragment (optional): M NBR atom_no To specify a root atom
for a ligand fragment (optional): M ROOT atom_no The “M” records (M SPLT, M
NBR, M ROOT) can alternatively be specified in a separate control file, which
can be used with MOL2 format files. Expects that the input ligand has already
had aromaticity “perceived”, i.e. that it contains aromatic bonds rather than
alternating single and double bonds (Kekule structure). Optionally writes a
kinemage graphics visualization of the atom tree, neighbor atom selection,
fragments, etc — very helpful for debugging and for visualizing exactly what
was done to the ligand.

Options:
-h, –help show this help message and exit
-n NM, –name=NM name ligand residues NM1,NM2,… instead of
LG1,LG2,…
-p FILE, –pdb=FILE prefix for PDB file names
-c, –centroid write files for Rosetta centroid mode too
–center=X,Y,Z translate output PDB coords to have given heavy-atom
centroid
-m MAX, –max-confs=MAX
don’t expand proton chis if above this many total
confs
-k FILE, –kinemage=FILE
write ligand topology to FILE
-a ALA, –amino-acid=ALA
set up params file for modified amino acid; .mol2
only; edit chis afterward. Implies –keep-names.
–clobber overwrite existing files
–no-param skip writing .params files (for debugging)
–no-pdb skip writing .pdb files (for debugging)
–keep-names leaves atom names untouched except for duplications
–recharge=CHG ignore existing partial charges, setting total charge
to CHG
–m-ctrl=FILE read additional M control lines from FILE