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ligand docking with rosetta_scripts.linuxgccrelease

Small Molecules

I installed the latest rosetta common (rosetta_src_2015.05.57576_bundle.tgz) and tried the following demo with error:

setting ligand_soft_rep weight hack_elec to 0.42

ERROR: unrecognized score_type type hack_elec
ERROR:: Exit from: src/core/scoring/ line: 477

Error: ERROR: Exception caught by JobDistributor while trying to get pose from job '1HXW_input_0001'

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metal_ions formal charge question

Small Molecules

Quick question: I've noticed that some of the .params files in residue_types/metal_ions have a "formal charge entry" such as for Zn: CHARGE ZN FORMAL +2, but some other divalent cations like Co lack this entry.

Is this entry even used by Rosetta?
Could some of these entries be incorrect?
Should the formal charge entry be added if I want to use that metal ion?


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Combine flags file with command line arguments?

Structure prediction
Enzyme Design
Loop Modeling
Small Molecules
Chemically Modified Residues
Fragment Generation
Non-Canonical Peptides
Nucleic Acids
Phenix / MR Rosetta

Is it possible to combine a flags file with command line arguments?

For example, something like this:

minimize_with_cst.linuxgccrelease -in:file:l min_pdb_file_list @flags_file

where flags_file contains additional options. Moreover, what is the effect of changing the order of command line arguments and flags files? Which takes precedence? That is, what is the difference between the above command and:

minimize_with_cst.linuxgccrelease @flags_file -in:file:l min_pdb_file_list


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Incorporating iron-sulfur cluster into ROSETTA applications

Small Molecules


I am working with an enzyme that uses Fe4S4 iron-sulfur clusters as co-factors. I recently built a model (using other software) and want to use ROSETTA for optimisation and enzyme design. I am very new to the software suite, and have managed to relax the protein together with the substrate ligand, for which I have a mol2 file. I would also like to include the iron-sulfur cluster, for which I have PDB coordinates, as well as AMBER PREP and FRCMOD files.

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