hydrogen_bond.py Command Help

Command: $SCHRODINGER/jaguar run hydrogen_bond.py

usage: $SCHRODINGER/jaguar run hydrogen_bond.py [-h] [-noopt] [-noopt_complex]
                                                [-noopt_torsions] [-fast]
                                                [-nocorr] [-WAIT] [-DEBUG]
                                                [-jobname <name>] [-subdir]
                                                [-recover] [-no_subjob_files]
                                                [-scr <absolute path>]
                                                [-PARALLEL <N>]
                                                [-max_threads <T>]
                                                [-procs_per_node <N>]
                                                [-use_one_node | -use_multiple_nodes]
                                                [-HOST <host>:<M>]
                                                [-SUBHOST <host>:<M>] [-SAVE]
                                                [-NOJOBID]
                                                [-OPLSDIR <oplsdir>]
                                                infiles [infiles ...]

Calculate the binding energy of a hydrogen-bonded pair of
molecules by a protocol adapted from that described in Kaminski, et
al. J. Chem. Theory Comput. 1 (2005) 248-254.

positional arguments:
  infiles               Maestro or Jaguar input file(s)

options:
  -h, --help            show this help message and exit
  -noopt                Don't perform any geometry optimizations
  -noopt_complex        Don't optimize geometry of full complex
  -noopt_torsions       Freeze all torsions during optimizations
  -fast                 Fast mode: just use DFT energies to calculate binding energy
  -nocorr               Don't apply final energy corrections or extrapolations

other options:
  -WAIT                 Wait for job to finish before returning prompt.
  -DEBUG, -D            Print detailed information about job launch.
  -jobname <name>       Set the job name.
  -subdir               Run Jaguar in a sub-directory.
  -recover              Manually re-run a job using the recover mechanism. NOTE this option is not recommended for default recovery jobs.
                        Use "jaguar run <filename>.recover" instead (see documentation for more details).
  -no_subjob_files      Do not return subjob output files to launch directory.
  -scr <absolute path>  Specify a scratch directory (must not already exist). Directory must be given as an absolute path.
                        Note this will be used by the Fortran backend and is independent of the specification of -TMPDIR.
  -PARALLEL <N>         Use up to <N> CPUs simultaneously for the whole workflow, automatically allocated among subjobs, including threaded subjobs.
  -max_threads <T>      Use no more than <T> OpenMP threads for each Jaguar subjob. Default 8.
  -procs_per_node <N>   Use no more than <N> CPUs per node. Default is taken from the schrodinger.hosts file; if undefined 8.
  -use_one_node         Force CPU resources to be requested upfront on one node. 
                        This pool of CPUs will be used for the duration of the job instead of resubmitting to the queue.
  -use_multiple_nodes   Force CPU resources to be requested dynamically from the queue (if available) instead of upfront on one node.

commonly used Schrodinger Suite options:
  -HOST <host>:<M>      Run job remotely on host <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs. 
                        May be combined with -PARALLEL <N>.
  -SUBHOST <host>:<M>   Run any subjobs remotely on subhost <hostname>. The optional :<M> defines the maximum number of simultaneous subjobs. 
                        May be combined with -PARALLEL <N>.
  -SAVE                 Return .zip file of scratch directory.
  -NOJOBID              Run Jaguar interactively without jobserver (not available with python workflows).
  -OPLSDIR <oplsdir>    Use custom FF parameters from specified directory for workflows which support it.