usage

Usage example

Run

../../build/nrgmin --setup-json setup.json

The output will be in files out.pdb and out.json, which contains energy terms. setup.json has three minimization stages and out.json will record final energy values for each stage and each model. If you want to print every step, for example you can run

../../build/nrgmin --setup-json setup.json --print-step

Or add "print_step": true to "options" field in setup.json and rerun

../../build/nrgmin --setup-json setup.json

Setup.json explained

The field options can contain all the flags listed in --help. Flags added to options will act globally, meaning that every minimization stage added to stages will use the value from options unless specified differently.

"options": {
    "rec_pdb": "BACE_4_rec_2models.pdb",
    "rec_psf": "BACE_4_rec.psf",
    "rec_prm": "BACE_4_rec_parm.prm",
    "rec_rtf": "BACE_4_rec_pdbamino.rtf",
    "lig_json": "BACE_4_lig.json",
    "lig_pdb": "BACE_4_lig_2models_close.pdb"
}

The above setup can be reproduced by using all the same flags via the command line:

../../build/nrgmin --rec-pdb BACE_4_rec_2models.pdb --rec-psf BACE_4_rec.psf --rec-prm BACE_4_rec_parm.prm --rec-rtf BACE_4_rec_pdbamino.rtf --lig-json BACE_4_lig.json --lig-pdb BACE_4_lig_2models_close.pdb 

The field stages is optional and can be added if you want to define separate minimization stages with different parameters. For example, if you want to run 500 steps with the fixed ligand, and then 500 steps without torsions you can use the following:

{
    "options": {
        "rec_pdb": "BACE_4_rec_2models.pdb",
        "rec_psf": "BACE_4_rec.psf",
        "rec_prm": "BACE_4_rec_parm.prm",
        "rec_rtf": "BACE_4_rec_pdbamino.rtf",
        "lig_json": "BACE_4_lig.json",
        "lig_pdb": "BACE_4_lig_2models_close.pdb"
    },
    "stages": [
        {
            "nsteps": 500,
            "fix_ligand": true
        },
        {
            "nsteps": 500,
            "dihedrals": false
        }
    ]
}

This will be equivalent to specifying nsteps globally:

{
    "options": {
        "rec_pdb": "BACE_4_rec_2models.pdb",
        "rec_psf": "BACE_4_rec.psf",
        "rec_prm": "BACE_4_rec_parm.prm",
        "rec_rtf": "BACE_4_rec_pdbamino.rtf",
        "lig_json": "BACE_4_lig.json",
        "lig_pdb": "BACE_4_lig_2models_close.pdb",
        "nsteps": 500
    },
    "stages": [
        {
            "fix_ligand": true
        },
        {
            "dihedrals": false
        }
    ]
}