- -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.
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