hbond_basicity_predictor.py Command Help
Command: $SCHRODINGER/jaguar run hbond_basicity_predictor.py
usage: $SCHRODINGER/jaguar run hbond_basicity_predictor.py [-h]
[-basis_set BASIS_SET]
[-functional FUNCTIONAL]
[-H H] [-Cl CL]
[-Br BR] [-I I]
[-ppa PPA]
[-extend EXTEND]
[-esp_method {jaguar,xtb}]
[-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>]
infile outfile
This script implements the Va(r) method of Peter Kenny for evaluating hydrogen-
bond donor strengths and detects local minima, Vmin, in a cubic ESP grid around
the molecule.
It has been extended to compute the ESP values for halogen bond donors not at
0.002 a.u. electron density point, as done by Zou et al., but using a fixed
distance that correlates reasonably well with the ESP values obtained in that
paper.
The locations where the raw ESP values are evaluated are added to each molecule
as a dummy atom. The value can be shown by displaying the label using the
'Kenny ESP' atom properties for those atoms.
Note:
1) The default r for hydrogen bonds is a lot smaller than its van der Waals
radius, which are used for halogen bonds, so comparison between the H and
halogens is not possible.
2) The code assumes that the input geometries are correct.
References:
1. Peter Kenny. J. Chem. Inf. Model., 2009, 49 (5), pp 1234-1244 (https://doi.org/10.1021/ci9000234)
2. Jian-Wei Zou, Meilan Huang, Gui-Xiang Hu and Yong-Jun Jiang, RSC Adv., 2017,
7, 10295-10395 (https://doi.org/10.1039/C6RA27590G)
Copyright Schrodinger, LLC. All rights reserved.
positional arguments:
infile Input structure .mae file (can contain multiple structures).
outfile Output .mae structure file.
options:
-h, --help show this help message and exit
-basis_set BASIS_SET Basis set. (default: LACVP**+)
-functional FUNCTIONAL
Functional. (default: B3LYP)
-H H Distance from H to evaluate the ESP along the R-H vector in Å. (default 0.55)
-Cl CL Distance from Cl to evaluate the ESP along the R-Cl vector in Å. (default 1.75)
-Br BR Distance from Br to evaluate the ESP along the R-Br vector in Å. (default 1.85)
-I I Distance from I to evaluate the ESP along the R-I vector in Å. (default 1.98)
-ppa PPA Number of ESP points per Å. (Default 5)
-extend EXTEND Amount that the bounding box for the atom should be extended in Å. (default 3.0)
-esp_method {jaguar,xtb}
Method to use for computing ESP. Options are jaguar, xtb.
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.