rosetta residue topology file
NAME ALA
NAME The name of the Residue. Must be unique among all residues loaded into Rosetta
IO_STRING ALA A
IO_STRING The 3 letter and 1 letter codes representing the residue. 3 letter code is not unique; it does not need to be the same as the name. 1 letter code is Z by default.
TYPE POLYMER #residue type
TYPE The type of residue being represented, should be ‘LIGAND’ for ligands, or ‘POLYMER’ for amino acids, DNA and RNA bases, or other polymer building-blocks.
AA ALA
AA The amino acid type. Should be “UNK” for ligands, or for most non-canonicals. (Note that this corresponds to the core::chemical::AA enum, internally.)
ROTAMER_AA ALA
ATOM N Nbb NH1 -0.47 -0.350
ATOM CA CAbb CT1 0.07 0.100
ATOM C CObb C 0.51 0.550
ATOM O OCbb O -0.51 -0.550
ATOM CB CH3 CT3 -0.27 0.000
ATOM H HNbb H 0.31 0.250
ATOM HA Hapo HB 0.09 0.000
ATOM 1HB Hapo HA 0.09 0.000
ATOM 2HB Hapo HA 0.09 0.000
ATOM 3HB Hapo HA 0.09 0.000
The first column after the ATOM specifier is the atom name, and the second column (the Nbb/CAbb/etc.) is the Rosetta atom type. The third column (NH1/CT1/C/O) is the CHARMM molecular mechanics atom type, which is not used by default in Rosetta, but is read by certain specialty energy terms (the “MM” terms). (The fourth and fifth columns are partial charges.)
LOWER_CONNECT N
UPPER_CONNECT C
CONNECT Gives an atom a connection to an (unspecified) atom in another residue. This is not to be used for the N and C in the backbone; those are given with LOWER_CONNECT and UPPER_CONNECT respectively.
BOND N CA
BOND N H
BOND CA C
BOND CA CB
BOND CA HA
BOND_TYPE C O 2
BOND CB 1HB
BOND CB 2HB
BOND CB 3HB
BOND Defines a bond connection between two named atoms.
PROPERTIES PROTEIN CANONICAL_AA ALPHA_AA L_AA METALBINDING ALIPHATIC
METAL_BINDING_ATOMS O
PROPERTIES A series of properties describing this ligand type or residue type. Allowed properties include (though this list is not exhaustive): PROTEIN POLYMER LIGAND COARSE METAL METALBINDING DNA RNA CARBOHYDRATE SURFACE POLAR CHARGED AROMATIC TERMINUS LOWER_TERMINUS UPPER_TERMINUS SC_ORBITALS. For an exhaustive list of allowed properties, see the file source/src/core/chemical/residue_properties/general_properties.list in the main Rosetta repository.
NBR_ATOM CB
NBR_ATOM The PDB name of the “neighbor atom”. In the case of ligands, this defaults to the atom that is closest to the geometric center of the ligand
#APL O to CB DISTANCE – MAX O-CB OBSERVED IN UBQ
NBR_RADIUS 3.4473
NBR_RADIUS The radius of gyration of the ligand, used to define the overall size of the ligand.
FIRST_SIDECHAIN_ATOM CB
RAMA_PREPRO_FILENAME scoring/score_functions/rama/fd/all.ramaProb scoring/score_functions/rama/fd/prepro.ramaProb
ACT_COORD_ATOMS CB END
ICOOR_INTERNAL N 0.000000 0.000000 0.000000 N CA C
ICOOR_INTERNAL CA 0.000000 180.000000 1.458001 N CA C
ICOOR_INTERNAL C 0.000000 68.800003 1.523258 CA N C
ICOOR_INTERNAL UPPER 149.999985 63.800007 1.328685 C CA N
ICOOR_INTERNAL O -180.000000 59.200005 1.231015 C CA UPPER
ICOOR_INTERNAL CB -122.800000 69.625412 1.521736 CA N C
ICOOR_INTERNAL 1HB -180.000000 70.500000 1.090040 CB CA N
ICOOR_INTERNAL 2HB 120.000000 70.500000 1.090069 CB CA 1HB
ICOOR_INTERNAL 3HB 120.000000 70.500000 1.088803 CB CA 2HB
ICOOR_INTERNAL HA -119.000000 71.900000 1.090078 CA N CB
ICOOR_INTERNAL LOWER -150.000000 58.300003 1.328685 N CA C
ICOOR_INTERNAL H -180.000000 60.849998 1.010000 N CA LOWER
ICOOR_INTERNAL The internal coordinates of an atom. The format goes backwards and looks like this:
And the fields are the following:
● Child atom
● phi angle (torsion angle between A1, A2, A3, A4)
● theta angle (improper angle = (180 - (angle between A4, A3, A2)))
● distance (between A4 and A3)
● parent atom
● angle atom
● torsion atom