Adding centroid .params files for non-canonical residues based on all-atom .params files

“Does anyone know how to create a centroid params file from scratch?”

From scratch – I’m tempted to say “you must first invent the universe”.

I’m going to send this along to the GenKIC developer, but broadly, you can get centroid params by taking a fullatom params and converting all the atom types to their closest equivalent in the centroid atom types list, or deleting them when appropriate.  There should be a centroid atom type set just like there’s a fullatom one (Rosetta/main/database/chemical/atom_type_sets/centroid).

I know that the molfile_to_params.py script used to make fullatom params has a flag for centroid mode. I don’t know if the polymeric version you may have used also has a centroid flag.

“Does anyone know how to create a centroid params file from scratch?”

From scratch – I’m tempted to say “you must first invent the universe”.

I’m going to send this along to the GenKIC developer, but broadly, you can get centroid params by taking a fullatom params and converting all the atom types to their closest equivalent in the centroid atom types list, or deleting them when appropriate.  There should be a centroid atom type set just like there’s a fullatom one (Rosetta/main/database/chemical/atom_type_sets/centroid).

I know that the molfile_to_params.py script used to make fullatom params has a flag for centroid mode. I don’t know if the polymeric version you may have used also has a centroid flag.

“Does anyone know how to create a centroid params file from scratch?”

From scratch – I’m tempted to say “you must first invent the universe”.

I’m going to send this along to the GenKIC developer, but broadly, you can get centroid params by taking a fullatom params and converting all the atom types to their closest equivalent in the centroid atom types list, or deleting them when appropriate.  There should be a centroid atom type set just like there’s a fullatom one (Rosetta/main/database/chemical/atom_type_sets/centroid).

I know that the molfile_to_params.py script used to make fullatom params has a flag for centroid mode. I don’t know if the polymeric version you may have used also has a centroid flag.

I wrote GenKIC, but have never had a case in which I needed to use it for centroid poses.  It should work, provided, as you say, that you have params files.  I’d amend what @smlewis said a little bit: to make a centroid params file from a full atom, you need to:

• keep all the mainchain atoms.
• remove the sidechain atoms, and replace them with a single CEN pseudo-atom.
• keep the properties; remove the rotamer libraries.
• set ROTAMERS BASIC (to allow centroid-mode packer-based design).
• set the ICOOR for the CEN pseudo-atom (which determines its position relative to the backbone).
• set the CEN atom type (which determines its radius and “sponginess”)
• keep the rama_prepro filename lines
• discard the metalbinding and metalbinding atom lines (I’ve never tested the metalbinding code in centroid mode, and can’t guarantee that it will work)

The question is, what are you doing with noncanonicals that requires a centroid representation?  We currently have no noncanonical-compatible protocols that work in centroid mode, so GenKIC (which probably is centroid-compatible, unlike most noncanonical-compatible protocols) will definitely not be your biggest stumbling block.  You’d be well-advised to revise your approach to use only fullatom representations.  If you’re working in RosettaScripts, ensure that the input to GenKIC (whatever the previous mover returns, or whatever you load from disk if GenKIC is the first mover) is a fullatom pose.

I wrote GenKIC, but have never had a case in which I needed to use it for centroid poses.  It should work, provided, as you say, that you have params files.  I’d amend what @smlewis said a little bit: to make a centroid params file from a full atom, you need to:

• keep all the mainchain atoms.
• remove the sidechain atoms, and replace them with a single CEN pseudo-atom.
• keep the properties; remove the rotamer libraries.
• set ROTAMERS BASIC (to allow centroid-mode packer-based design).
• set the ICOOR for the CEN pseudo-atom (which determines its position relative to the backbone).
• set the CEN atom type (which determines its radius and “sponginess”)
• keep the rama_prepro filename lines
• discard the metalbinding and metalbinding atom lines (I’ve never tested the metalbinding code in centroid mode, and can’t guarantee that it will work)

The question is, what are you doing with noncanonicals that requires a centroid representation?  We currently have no noncanonical-compatible protocols that work in centroid mode, so GenKIC (which probably is centroid-compatible, unlike most noncanonical-compatible protocols) will definitely not be your biggest stumbling block.  You’d be well-advised to revise your approach to use only fullatom representations.  If you’re working in RosettaScripts, ensure that the input to GenKIC (whatever the previous mover returns, or whatever you load from disk if GenKIC is the first mover) is a fullatom pose.

I wrote GenKIC, but have never had a case in which I needed to use it for centroid poses.  It should work, provided, as you say, that you have params files.  I’d amend what @smlewis said a little bit: to make a centroid params file from a full atom, you need to:

• keep all the mainchain atoms.
• remove the sidechain atoms, and replace them with a single CEN pseudo-atom.
• keep the properties; remove the rotamer libraries.
• set ROTAMERS BASIC (to allow centroid-mode packer-based design).
• set the ICOOR for the CEN pseudo-atom (which determines its position relative to the backbone).
• set the CEN atom type (which determines its radius and “sponginess”)
• keep the rama_prepro filename lines
• discard the metalbinding and metalbinding atom lines (I’ve never tested the metalbinding code in centroid mode, and can’t guarantee that it will work)

The question is, what are you doing with noncanonicals that requires a centroid representation?  We currently have no noncanonical-compatible protocols that work in centroid mode, so GenKIC (which probably is centroid-compatible, unlike most noncanonical-compatible protocols) will definitely not be your biggest stumbling block.  You’d be well-advised to revise your approach to use only fullatom representations.  If you’re working in RosettaScripts, ensure that the input to GenKIC (whatever the previous mover returns, or whatever you load from disk if GenKIC is the first mover) is a fullatom pose.