# Example Commands¶

POSIT always requires a bound-ligand in a receptor to fit against and an output file. The ligand (or ligands) to fit is specified with the -dbase option or the -in option, and the structures to fit are specified with the -receptors. Multiple receptors can be input at a time, in fact this is the preferred mode of running POSIT.

Note

-dbase accepts only 3D molecules, normally generated by OMEGA.

-in accepts most formats and generates 3D conformations when applicable. When in doubt, use the -in option.

## Basic Usage¶

The basic form of running POSIT is to fit against multiple receptors. The best fit receptor will be chosen for the final pose. Assuming that you have made receptors and combined them as shown above:

> posit -receptors renin/receptors/*.oeb.gz renin/merged/*.oeb.gz -in renin/all.smi \
-docked_molecule_file results.sdf


Note

On Microsoft Windows systems, you need to expand the wildcard:

> posit -receptor renin\receptors\2IL2_b.rec.oeb.gz renin\receptors\2IL2_a.rec.oeb.gz \
renin\receptors\2IL2_c.rec.oeb.gz renin\receptors\2IKO.rec.oeb.gz \
renin\receptors\2IKU_a.rec.oeb.gz renin\receptors\2IKU_b.rec.oeb.gz \
renin\merged\2IKU_a.rec._merge_2IKO.rec.oeb.gz renin\merged\2IKO.rec._merge_2IKU_a.rec.oeb.gz \
-in renin\all.smi -docked_molecule_file results.sdf


All results are written to the specified output file.

Any predicted ligand that has a good probability but clashes with the protein will either be ignored or, if the -clashed_mol_file output is specified on the command line, it will be output to the specified file.

> posit -receptors renin/receptors/*.oeb.gz renin/merged/*.oeb.gz -in renin/all.smi \
-docked_molecule_file results.sdf


## Ignoring Nitrogen Stereo¶

By default, POSIT ignores nitrogen stereo to make it easier to dock input x-ray models which may be time-averaged resulting in planar nitrogens.

If desired, this flag can be set to false in order to only fit explicit nitrogen stereo:

> posit -receptors renin/receptors/*.oeb.gz renin/merged/*.oeb.gz -in all.smi \
-docked_molecule_file results.sdf -ignore_nitrogen_stereo false


Note

POSIT 1.0 defaulted to not ignoring nitrogen stereo. This was changed due to the nature of crystallographic structures tending to produce time-averaged planar nitrogens.

Sometimes you may see warnings like the following:

Warning: Input stereochemistry different from output after fitting
in: CCc1c(c(nc([nH+]1)N)N)c2ccc3c(c2)N(CCC3)CCCOC
out: CCc1c(c(nc([nH+]1)N)N)c2ccc3c(c2)[N@](CCC3)CCCOC
Warning: Input stereochemistry different from output after fitting
in: CCc1c(c(nc([nH+]1)N)N)c2ccc3c(c2)N(CCC3)CCCOC
out: CCc1c(c(nc([nH+]1)N)N)c2ccc3c(c2)[N@@](CCC3)CCCOC


These simply serve as a warning that stereochemistry was added or modified during the fitting/optimization process.

> posit -receptors renin/receptors/*.oeb.gz -in renin/ren1.smi \