MARTINIZE.py is a script to create Coarse Grain Martini input files of proteins, ready for use in the molecular dynamics simulations package Gromacs. For more information on the Martini forcefield, see: www.cgmartini.nl and read our papers: Monticelli et al., J. Chem. Theory Comput., 2008, 4(5), 819-834 de Jong et al., J. Chem. Theory Comput., 2013, DOI:10.1021/ct300646g
The input file (-f) should be a coordinate file in PDB or GROMOS format. The format is inferred from the structure of the file. The input can also be provided through stdin, allowing piping of structures. The input structure can have multiple frames/models. If an output structure file (-x) is given, each frame will be coarse grained, resulting in a multimodel output structure. Having multiple frames may also affect the topology. If secondary structure is determined internally, the structure will be averaged over the frames. Likewise, interatomic distances, as used for backbone bond lengths in Elnedyn and in elastic networks, are also averaged over the frames available.
If an output file (-o) is indicated for the topology, that file will be used for the master topology, using #include statements to link the moleculetype definitions, which are written to separate files. If no output filename is given, the topology and the moleculetype definitions are written to stdout.
The secondary structure plays a central role in the assignment of atom types and bonded interactions in MARTINI. Martinize allows specification of the secondary structure as a string (-ss), or as a file containing a specification in GROMACS' ssdump format (-ss). Alternatively, DSSP can be used for an on-the-fly assignment of the secondary structure. For this, the option -dssp has to be used giving the location of the executable as the argument. The option -collagen will set the whole structure to collagen. If this is not what you want (eg only part of the structure is collagen, you can give a secondary structure file/string (-ss) and specifiy collagen as "F". Parameters for collagen are taken from: Gautieri et al., J. Chem. Theory Comput., 2010, 6, 1210-1218. With multimodel input files, the secondary structure as determined with DSSP will be averaged over the frames. In this case, a cutoff can be specified (-ssc) indicating the fraction of frames to match a certain secondary structure type for designation.
Several options are available to tune the resulting topology. By default, termini are charged, and chain breaks are kept neutral. This behaviour can be changed using -nt and -cb, respectively.
Disulphide bridges can be specified using -cys. This option can be given multiple times on the command line. The argument is a pair of cysteine residues, using the format chain/resn/resi,chain/resn/resi. It is also possible to let martinize detect cysteine pairs based on a cut-off distance of 0.22nm, by giving the keyword 'auto' as argument to -cys. Alternatively, a different cut-off distance can be specified, which will also trigger a search of pairs satisfying the distance criterion (eg: -cys 0.32).
In addition to cystine bridges, links between other atoms can be specified using -link. This requires specification of the atoms, using the format chain/resi/resn/atom,chain/resi/resn/atom,bondlength,forceconstant. If only two atoms are given, a constraint will be added with length equal to the (average) distance in the coordinate file. If a bond length is added, but no force constant, then the bondlength will be used to set a constraint.
Linking atoms requires that the atoms are part of the same moleculetype. Therefore any link between chains will cause the chains to be merged. Merges can also be specified explicitly, using the option -merge with a comma-separated list of chain identifiers to be joined into one moleculetype. The option -merge can be used several times. Note that specifying a chain in several merge groups will cause all chains involved to be merged into a single moleculetype.
The moleculetype definitions are written to topology include (.itp) files, using a name consisting of the molecule class (e.g. Protein) and the chain identifier. With -name a name can be specified instead. By default, martinize only writes a moleculetype for each unique molecule, inferred from the sequence and the secondary structure definition. It is possible to force writing a moleculetype definition for every single molecule, using -sep.
The option -p can be used to write position restraints, using the force constant specified with -pf, which is set to 1000 kJ/mol by default.
For stability, elastic bonds are used to retain the structure of extended strands. The option -ed causes dihedrals to be used instead.
Different forcefields can be specified with -ff. All the parameters and options belonging to that forcefield will be set (eg. bonded interactions, BB-bead positions, Elastic Network, etc.). By default martini 2.1 is used.
Martinize can write an elastic network for atom pairs within a cutoff distance. The force constant (-ef) and the upper distance bound (-eu) can be speficied. If a force field with an intrinsic Elastic network is specified (eg. Elnedyn) with -ff, -elastic in implied and the default values for the force constant and upper cutoff are used. However, these can be overwritten.
Martinize can process a structure to yield a multiscale system, consisting of a coordinate file with atomistic parts and corresponding, overlaid coarsegrained parts. For chains that are multiscaled, rather than writing a full moleculetype definition, additional [atoms] and [virtual_sitesn] sections are written, to be appended to the atomistic moleculetype definitions. The option -multi can be specified multiple times, and takes a chain identifier as argument. Alternatively, the keyword 'all' can be given as argument, causing all chains to be multiscaled.
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-f Input file (PDB|GRO)
-o Output topology (TOP)
-x Output coarse grained structure (PDB)
-n Output index file with CG (and multiscale) beads.
-nmap Output index file containing per bead mapping.
-v Verbose. Be load and noisy.
-h Display this help.
-ss Secondary structure (File or string)
-ssc Cutoff fraction for ss in case of ambiguity (default: 0.5).
-dssp DSSP executable for determining structure
-collagen Use collagen parameters -his Interactively set the charge of each His-residue. -nt Set neutral termini (charged is default) -cb Set charges at chain breaks (neutral is default) -cys Disulphide bond (+) -link Link (+) -merge Merge chains: e.g. -merge A,B,C (+) -name Moleculetype name -p Output position restraints (None/All/Backbone) (default: None) -pf Position restraints force constant (default: 1000 kJ/mol/nm^2) -ed Use dihedrals for extended regions rather than elastic bonds) -sep Write separate topologies for identical chains. -ff Which forcefield to use: -elastic Write elastic bonds -ef Elastic bond force constant Fc -el Elastic bond lower cutoff: F = Fc if rij < lo -eu Elastic bond upper cutoff: F = 0 if rij > up -ea Elastic bond decay factor a -ep Elastic bond decay power p -em Remove elastic bonds with force constant lower than this -eb Comma separated list of bead names for elastic bonds -multi Chain to be set up for multiscaling (+)