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Chris Brasnett edited this page Jul 26, 2024
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The full help menu for the most recent version martinize2 (July 2024) is recorded below.
The aim of this wiki is to be a practical guide to enable users to understand how to link these commands together to make their desired Martini model of their protein, ready to simulate.
Throughout these pages, we assume you have a clean input file, protein.pdb, at
atomistic resolution, ready to convert into a system ready to simulate at Martini resolution.
Consume your Martinis safely!
usage: martinize2 [-h] [-V] [-f INPATH] [-x OUTPATH] [-o TOP_PATH] [-sep] [-merge MERGE_CHAINS] [-resid RESID_HANDLING] [-ignore IGNORE_RES [IGNORE_RES ...]]
[-ignh] [-model MODELIDX] [-bonds-from {name,distance,none,both}] [-bonds-fudge BONDS_FUDGE] [-ff TO_FF] [-from FROM_FF]
[-ff-dir EXTRA_FF_DIR] [-map-dir EXTRA_MAP_DIR] [-list-ff] [-list-blocks] [-p {none,all,backbone}] [-pf POSRES_FC] [-dssp [DSSP] | -ss
SEQUENCE | -collagen] [-ed] [-elastic] [-ef RB_FORCE_CONSTANT] [-el RB_LOWER_BOUND] [-eu RB_UPPER_BOUND] [-ermd RES_MIN_DIST]
[-ea RB_DECAY_FACTOR] [-ep RB_DECAY_POWER] [-em RB_MINIMUM_FORCE] [-eb RB_SELECTION] [-eunit RB_UNIT] [-go GO] [-go-eps GO_EPS]
[-go-moltype GOVS_MOLTYPE] [-go-low GO_LOW] [-go-up GO_UP] [-go-res-dist GO_RES_DIST] [-water-bias]
[-water-bias-eps WATER_BIAS_EPS [WATER_BIAS_EPS ...]] [-id-regions WATER_IDRS [WATER_IDRS ...]] [-idr-tune] [-scfix] [-cys CYSTEIN_BRIDGE]
[-mutate MUTATIONS] [-modify MODIFICATIONS] [-nter MODIFICATIONS] [-cter MODIFICATIONS] [-nt] [-write-graph WRITE_GRAPH]
[-write-repair WRITE_REPAIR] [-write-canon WRITE_CANON] [-v] [-maxwarn MAXWARN [MAXWARN ...]]
options:
-h, --help show this help message and exit
-V, --version show program's version number and exit
Input and output files:
-f INPATH Input file (PDB|GRO) (default: None)
-x OUTPATH Output coarse grained structure (PDB) (default: None)
-o TOP_PATH Output topology (TOP) (default: None)
-sep Write separate topologies for identical chains (default: False)
-merge MERGE_CHAINS Merge chains: either a comma separated list of chains to merge e.g. -merge A,B,C (+), or -merge all if instead all chains in the
input file should be merged. Can be given multiple times for different groups of chains to merge. (default: None)
-resid RESID_HANDLING
How to handle resid. Choice of mol or input. mol: resids are numbered from 1 to n for each molecule input: resids are the same as in
the input pdb (default: mol)
-ignore IGNORE_RES [IGNORE_RES ...]
Ignore residues with that name: e.g. -ignore HOH,LIG (+) (default: [])
-ignh Ignore all Hydrogen atoms in the input file (default: False)
-model MODELIDX Which MODEL to select. Only meaningful for PDB files. (default: None)
-bonds-from {name,distance,none,both}
How to determine connectivity in the input. If 'none', only bonds from the input file (CONECT) will be used. (default: both)
-bonds-fudge BONDS_FUDGE
Factor with which Van der Waals radii should be scaled when determining bonds based on distances. (default: 1.2)
Force field selection:
-ff TO_FF Which forcefield to use (default: martini3001)
-from FROM_FF Force field of the original structure. (default: charmm)
-ff-dir EXTRA_FF_DIR Additional repository for custom force fields. (default: [])
-map-dir EXTRA_MAP_DIR
Additional repository for mapping files. (default: [])
-list-ff List all known force fields, and exit. (default: False)
-list-blocks List all Blocks and Modifications known to the force field, and exit. (default: False)
Position restraints:
-p {none,all,backbone}
Output position restraints (none/all/backbone) (default: none)
-pf POSRES_FC Position restraints force constant in kJ/mol/nm^2 (default: 1000)
Secondary structure handling:
-dssp [DSSP] DSSP executable for determining structure. If this flag is givenbut no executable is specified, the mdtraj library will be usedto
compute the secondary structure, if it can be imported. (default: None)
-ss SEQUENCE Manually set the secondary structure of the proteins. Either give a dssp sequence for each residue in your input file or a single
letter to be repeated for the entire sequence, e.g. -ss C (default: None)
-collagen Use collagen parameters (default: False)
-ed Use dihedrals for extended regions rather than elastic bonds (default: False)
Protein elastic network:
-elastic Write elastic bonds (default: False)
-ef RB_FORCE_CONSTANT
Elastic bond force constant Fc in kJ/mol/nm^2 (default: 500)
-el RB_LOWER_BOUND Elastic bond lower cutoff: F = Fc if rij < lo (default: 0)
-eu RB_UPPER_BOUND Elastic bond upper cutoff: F = 0 if rij > up (default: 0.9)
-ermd RES_MIN_DIST The minimum separation between two residues to have an RB the default value is set by the force-field. (default: None)
-ea RB_DECAY_FACTOR Elastic bond decay factor a (default: 0)
-ep RB_DECAY_POWER Elastic bond decay power p (default: 1)
-em RB_MINIMUM_FORCE Remove elastic bonds with force constant lower than this (default: 0)
-eb RB_SELECTION Comma separated list of bead names for elastic bonds (default: None)
-eunit RB_UNIT Establish what is the structural unit for the elastic network. Bonds are only created within a unit. Options are molecule, chain,
all, or aspecified region defined by resids, with followingformat: <start_resid_1>:<end_resid_1>, <start_resid_2>:<end_resid_2>...
(default: molecule)
Virtual site based GoMartini:
-go GO Contact map to be used for the Martini Go model. Currently, only one format is supported. See docs. (default: None)
-go-eps GO_EPS The strength of the Go model structural bias in kJ/mol. (default: 9.414)
-go-moltype GOVS_MOLTYPE
Set the name of the molecule when using Virtual Sites GoMartini. (default: molecule_0)
-go-low GO_LOW Minimum distance (nm) below which contacts are removed. (default: 0.3)
-go-up GO_UP Maximum distance (nm) above which contacts are removed. (default: 1.1)
-go-res-dist GO_RES_DIST
Minimum graph distance (similar sequence distance) below whichcontacts are removed. (default: 3)
Apply water bias.:
-water-bias Automatically apply water bias to different secondary structure elements. (default: False)
-water-bias-eps WATER_BIAS_EPS [WATER_BIAS_EPS ...]
Define the strength of the water bias by secondary structure type. For example, use `H:3.6 C:2.1` to bias helixes and coils. Using
the idr option (e.g. idr:2.1) intrinsically disordered regions are biased seperately. (default: [])
-id-regions WATER_IDRS [WATER_IDRS ...]
Intrinsically disordered regions specified by resid.These parts are biased differently when applying a water bias.format:
<start_resid_1>:<end_resid_1> <start_resid_2>:<end_resid_2>... (default: [])
-idr-tune Tune the idr regions with specific bonded potentials. (default: False)
Protein description:
-scfix Apply side chain corrections. (default: False)
-cys CYSTEIN_BRIDGE Cystein bonds (default: none)
-mutate MUTATIONS Mutate a residue. Desired mutation is specified as, e.g. A-PHE45:ALA. The format is <chain>-<resname><resid>:<new resname>. Elements
of the specification can be omitted as required.e.g. PHE45:ALA will mutate all PHE with resid 45 to ALA, A-PHE:ALA will mutate all
PHE on chain A to ALA (default: [])
-modify MODIFICATIONS
Add a modification to a residue. Desired modification is specified as, e.g. A-ASP45:ASP0. The format is
<chain>-<resname><resid>:<modification>. Elements of the specification can be omitted as required. e.g. ASP45:ASP0 will modify all
ASP with resid 45 to ASP0, A-ASP:ASP0 will modify all ASP on chain A to ASP0 (default: [])
-nter MODIFICATIONS Shorthand for patching N-termini. An N-terminus is defined as a residue which is connected to 1 other residue, and has the highest
resid. (default: [])
-cter MODIFICATIONS Shorthand for patching C-termini. A C-terminus is defined as a residue which is connected to 1 other residue, and has the lowest
resid. (default: [])
-nt Set neutral termini (charged is default). Alias for "-nter NH2-ter -cter COOH-ter" (default: False)
Debugging options:
-write-graph WRITE_GRAPH
Write the graph as PDB after the MakeBonds step. (default: None)
-write-repair WRITE_REPAIR
Write the graph as PDB after the RepairGraph step. The resulting file may contain "nan" coordinates making it unreadable by most
softwares. (default: None)
-write-canon WRITE_CANON
Write the graph as PDB after the CanonicalizeModifications step. The resulting file may contain "nan" coordinates making it
unreadable by most software. (default: None)
-v Enable debug logging output. Can be given multiple times. (default: 0)
-maxwarn MAXWARN [MAXWARN ...]
The maximum number of allowed warnings. If more warnings are encountered no output files are written. (default: [])