dps pdb2bond

Add PDB CONECT records from a DROPPS run file or system topology.

Synopsis and options

usage: dps pdb2bond [-h] (-s FILE | -p FILE) -f FILE -o FILE [-noa]

Add PDB CONECT records from a DROPPS run file or system topology.

Input:
  -s FILE, --run-input FILE
                        Input DROPPS run file (.tpr) containing system bonds. (required: choose
                        one option from this group)
  -p FILE, --topology FILE
                        Input system topology file (.top) containing system bonds. (required:
                        choose one option from this group)
  -f FILE, --input FILE
                        Input structure file (.pdb). (required)

Output:
  -o FILE, --output FILE
                        Output structure file (.pdb) containing CONECT records. (required)

Parameters:
  -h, --help            Show this help message and exit.
  -noa, --preserve-atom-types
                        Preserve input element fields instead of writing every bead as carbon.
                        (default: False)

Examples:
  dps pdb2bond -s run.tpr -f frame.pdb -o bonded.pdb

Note

This page is generated from the DROPPS 1.0 argument parser. Run dps pdb2bond -h in the installed environment for the same reference at the command line.