Posit How to

Ignore Nitrogen stereo

Nitrogen stereo can be ignored in Posit by setting the -ignore_nitrogen_stereo parameter to true.

Prepare molecules for Posit

With default settings, Posit internally generates the required input conformers and Posit can be used with 2D input molecules. However, if it is desired to pass a pre-generated set of conformers to Posit, following are the recommended ways to supply or prepare molecules for POSIT.

1. Use OMEGA or the OMEGA toolkit to prepare molecules or expand the stereo chemistry using OEFlipper. POSIT is guaranteed to work correctly if the input molecules have been generated by OMEGA.

2. Pass the OMEGA generated 3D conformers through the -dbase parameter. This method of running POSIT is not recommended as a large portion of the flexible methodology will be deactivated.

Use multiple receptors

Multiple receptors can be passed to Posit through the -receptor command-line parameter.

Obtain clash-free pose

Pose generated from Posit with the default options can sometimes contain clashes. Users have the option to perform pose relaxation, either on the clashed poses or on all generated poses, with the -relax command-line parameter