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basic_usage
Without any other additions, martinize2 can take your protein, and make a ready coarse grained model with some martini
forcefield:
martinize2 -f protein.pdb -o topol.top -x cg_protein.pdbThis command will (try) and convert your protein from the atomistic input to one in the Martini3 force field.
Other force fields are available to convert your protein to. To view them you can use martinize2 -list-ff.
However, our knowledge of proteins and Martini tells us that we need to add some more information to the topology to account for secondary structure.
Martinize2 can deal with secondary structure intelligently using dssp in one of two ways:
- Use a dssp executable installed on your machine
- Use the dssp implementation in mdtraj
If you have dssp installed locally, note that martinize2 is only validated for particular versions of dssp. If a
non-validated version is used, a warning will be raised and nothing is written. If you know what you're doing and are
confident with what's been produced, you can override the warning with the -maxwarn flag.
Otherwise, dssp can be used using the -dssp flag in martinize.
Where you have a local installation, replace /path/to/dssp in the following command with the location of your installation:
martinize2 -f protein.pdb -o topol.top -x cg_protein.pdb -ff martini3001 -dssp /path/to/dsspIf you have mdtraj installed in your python environment, the -dssp flag can be
left blank, and martinize2 will attempt to use dssp from there:
martinize2 -f protein.pdb -o topol.top -x cg_protein.pdb -ff martini3001 -dsspIf you already know the secondary structure of your protein and don't want to worry about
dssp calculating it correctly, the -ss flag can be used.
The -ss flag must either be:
- The same length as the number of residues in your protein, with a dssp code for each residue
- A single letter (eg. 'H'), which will apply the same secondary structure parameters to your entire protein