dps pdb2dps

Generate coarse-grained PDB conformations and an ITP topology from a protein sequence.

Synopsis and options

usage: dps pdb2dps [-h] -s SEQUENCE [-f FILE] [-ri RESIDUE_INDEX]
                   [-ptm POST_TRANSLATIONAL_MODIFICATION [POST_TRANSLATIONAL_MODIFICATION ...]]
                   [-r RADIUS] [-n NUMBER] [-e DEGREE_EXTEND] [--seed SEED]
                   [--max-attempts MAX_ATTEMPTS] [-ff {CALVADOS2,HPS,HPSRNA,HPST,MPiPi,MPiPi_PTM}]
                   [-oc FILE] [-op FILE] [-on NAME] [-cNTD] [-cCTD]

Generate coarse-grained PDB conformations and an ITP topology from a protein sequence.

Input:
  -s SEQUENCE, --sequence SEQUENCE
                        One-letter protein sequence. (required)
  -f FILE, --input-pdb FILE
                        Optional all-atom PDB file (.pdb) used to initialize C-alpha coordinates.
                        (default: None)

Output:
  -oc FILE, --output-conformation FILE
                        Output PDB path or prefix; multiple conformations use numbered .pdb files.
                        (default: None)
  -op FILE, --output-topology FILE
                        Output topology file (.itp); the extension is added if omitted. (default:
                        None)
  -on NAME, --output-name NAME
                        Molecule name written to the ITP topology. (default: MOL)

Parameters:
  -h, --help            Show this help message and exit.
  -ri RESIDUE_INDEX, --residue-index RESIDUE_INDEX
                        Residue number assigned to the first bead. (default: 1)
  -ptm POST_TRANSLATIONAL_MODIFICATION [POST_TRANSLATIONAL_MODIFICATION ...], --post-translational-modification POST_TRANSLATIONAL_MODIFICATION [POST_TRANSLATIONAL_MODIFICATION ...]
                        Post-translational modifications in ORIGINAL+NUMBER+MODIFIED form, for
                        example S129SMP. (default: None)
  -r RADIUS, --radius RADIUS
                        Maximum radius of gyration for a generated conformation, in nm. (default:
                        2.0)
  -n NUMBER, --number NUMBER
                        Number of conformations to generate. (default: 1)
  -e DEGREE_EXTEND, --degree-extend DEGREE_EXTEND
                        Chain-extension fraction between 0 and 1. (default: 0.5)
  --seed SEED           Random seed used for reproducible conformation generation. (default: 1215)
  --max-attempts MAX_ATTEMPTS
                        Maximum whole-chain construction attempts before failing. (default: 10000)
  -ff {CALVADOS2,HPS,HPSRNA,HPST,MPiPi,MPiPi_PTM}, --forcefield {CALVADOS2,HPS,HPSRNA,HPST,MPiPi,MPiPi_PTM}
                        Force field to use; if omitted, prompt interactively. (default: None)
  -cNTD, --charged-NTD  Add a positive charge patch to the N terminus. (default: False)
  -cCTD, --charged-CTD  Add a negative charge patch to the C terminus. (default: False)

Examples:
  dps pdb2dps -s MSEQNNTEMTFQIQRIYTKDISFEAPNAPHVFQKDW -oc chain.pdb -op chain.itp

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps pdb2dps -h in the installed environment for the same reference at the command line.