Required Parameters

-receptor <filenames>

List of receptors used to predict the pose of the input molecules. Receptors must include a bound ligand.

Multiple receptors can be input:

> posit -receptor rec*.oeb

Will use all files that start with rec and end with .oeb.

> posit -receptor  receptors.lst

Will use all receptors files specified in the receptors.lst file. If any entry in the specified file is not a valid receptor, POSIT will halt.

Supported -receptor file formats are:

File type Extension
OEBinary .oeb .oeb.gz
list .lst

Multiple receptor files and list files can be used simultaneously.

Note

This option also is aliased to -receptors.

-in <filename>

Input molecules to pose-predict. If 3D molecules are input, the original conformations are retained for optimization as well as the expanded conformational ensemble.

[ Aliases = -lig ]

POSIT uses an internal conformation sampling to generate high-quality conformations. However, input ring structures (chair/boat) may not be reproduced as POSIT may choose a lower energy ring template during the sampling process.

Supported input file formats are:

File type Extension
OEBinary .oeb .oeb.gz
SDF .sdf .mol .sdf.gz .mol.gz
MOL2 .mol2 .mol2.gz
PDB .pdb .ent .pdb.gz .ent.gz
MacroModel .mmod .mmod.gz
Smiles .smi .smi.gz .ism.gz