Prime Command Input File

Type of job to run. The available options are:

RMSD cutoff for eliminating redundant conformers, where relevant.

Required. Turn on or off closure of the chain breaks near deletions in the alignment. If not closed, they will remain as chain breaks in the output structure.

A string of integers indicating from which template (or, more specifically, from which alignment) coordinates for a given residue should be obtained. Thus, this string of integers must be equal in length to the query sequence being used in the alignment files. COMPOSITE_ARRAY is required for multiple template jobs. It is not required for single template jobs, but if it is present, it is ignored.

Required. Specifies which side chains to optimize. If true, the rotamers for conserved side chains are preserved, and only non-conserved side chains are predicted. If false, all side chains are predicted. This keyword is ignored if SIDE_OPT is false.

Specifies the longest insertion in the alignment that will be built. Insertions longer than this will be omitted, and not appear in the output structure. Residue numbering will reflect the full query sequence however. Default: 1000.

Fraction of van der Waals distance used to define a clash. Smaller values allow structures with worse potential atomic overlaps to be generated. Default: 0.70

Turn on or off a side chain optimization stage. Default: true.

Required if a ligand is present. Specifies a ligand to include from this template. The format of the specification is
AAA C:###

where AAA is the ligand’s three letter code, C is its chain ID, ### is its residue number. Multiple ligands from the template are numbered using i as an index, starting from zero.

Required. Used to identify a given template in the COMPOSITE_ARRAY (see below). Numbering goes from 1 to 9.

Add missing side chains in a default extended conformation. No sampling or refinement of the added side chains is performed.

Energy cutoff for return of conformations. Returns all conformations within value kcal/mol of the lowest-energy structure. It can be used in conjunction with NUM_OUTPUT_STRUCT, to impose a maximum on the number of such conformations to return. As with NUM_OUTPUT_STRUCT, it only applies to single loop refinements.

Dielectric constant of the continuum solvation model. Default: 80.0. Used with SGB_MOD sgbnp.

Fraction of van der Waals distance used to define a clash. Smaller values allow structures with worse potential atomic overlaps to be generated. Valid for LOOP_BLD and HELIX_BLD jobs. Default: 0.70

Specify a constraint on a pair of atoms. The format of the atom specifications is given at the beginning of this chapter. The value of dist is the target distance between the atoms in angstroms. The value of strength is the coefficient of the harmonic constraint potential in kcal mol⁻¹ Å⁻², which has a default value of 350.

Type of calculation to perform when running a refinement job (JOB_TYPE REFINE). The available options are:

Retain corrections made when duplicate residue numbers are found. The duplications detected are between non-protein residues or between protein and non-protein residues. The non-protein residue is assigned a new, unique chain name temporarily. If you set this keyword to yes, the new chain name is written to the output file. Default: no.

Specify the manner for specifying which residues to refine. Available options are:

Input structure file in Maestro format, compressed (.mae.gz, .maegz) or uncompressed (.mae). If the file contains multiple structures, each structure is refined, or the structures specified by ENTRY.

Indicates whether to use a random seed for the random number generator. This keyword has no effect on Minimization tasks. Default: no.

Constrain the specified residue to be buried (no more than 20% of surface area exposed to solvent).

Constrain the specified residue to be exposed (more than 40% of surface area exposed to solvent).

Build the specified sequence as an alpha helix. The format of the residue specifications spec1 and spec2 is given at the beginning of this chapter. You should include enough residues on either side of the helical region in the loop prediction to ensure that sufficient flexibility is available to build the loop.

Place the C-alpha atoms of the loop either inside or outside the membrane in the building stage. Refinement can move the residues across the membrane boundary.

Specify the maximum distance that any alpha carbon atom in the loop should be allowed to move during refinement stage 1 (Ref1). Omitting this parameter indicates that no restriction should be applied.

Maximum number of subjobs that can run at one time. This can be set to a value less than the value of THREADS if sufficient resources are not available. Not available with refinestruct.

Specify the number of stages in which backbones of residues at the beginning or end of the loop are fixed. These stages are inserted between the CA refinement stages. Each stage fixes progressively more residues, starting with 1. The fixed residues are distributed in all combinations between the ends of the loop, so, for example, stage 4 has 5 combinations and therefore 5 refinement jobs. Default: 5.

Type of refinement to be carried out. Can be specified as either a number or text string. Different from refinestruct. Available choices are:

0 or default: Equivalent to running a single loop refinement using refinestruct. Not particularly useful except for completeness and testing purposes. Does not recognize THREADS keyword.

1 or extended: Used for Extended Sampling from the GUI. Does not recognize MIN_OVERLAP and MAX_CA_MOVEMENT keywords, as these are used internally by the protocol. Accepts multiple loops as input which are run sequentially.

2 or long_loop: No longer used.

3 or loop_pair: Used for Cooperative Loop Sampling from the GUI. Exactly two loops must be specified.

4 or long_loop_2: Used for Ultra-extended Sampling from the GUI. Does not recognize the MAX_CA_MOVEMENT keyword, as this is used internally by the protocol. Only one loop can be specified.

Number of residues to include in the loop defined for backbone sampling in side-chain prediction. Only used with SAMPLE_BACKBONE. Default: 3.

Maximum angular displacement of the CA-CB vector from the initial position when sampling CB positions. Only used with SAMPLE_CBETA. Default: 30°.

Number of passes through side chain optimization of the protein residues followed by minimization of the protein residues (including the backbone). These two steps are repeated the specified number of times before proceeding to optimization of the protein and the ligand.
Default: 2. Files written from Maestro have NPASSES set to 1.

Specify helix and region containing helix. Values of i are:

A keyword with each value of i must be included in the input.

Maximum amount of movement allowed in the C terminus of the helix. Default: 5 Å.

Fraction of the distance from the start to the end of the helix that is used as the origin for rotation. Default: 0.5.

Maximum amount of roll sampled, in degrees. Default: 0.

Maximum number of minimization cycles for the solvent treatment. Each cycle consists of a minimization to the specified RMSD with a particular set of solvent parameters, after which the solvent parameters are updated. The iterative procedure finishes if the energy changes by less than 1 kcal/mol or the number of cycles is exceeded. Default: 2.