obprobe1

Usage

Overview

The obprobe tool creates a grid around a molecule, placing a probe atom with a specified atom type and partial charge at each point to calculate the MMFF94 energy. This can be used for docking experiments to test hydrogen-bond affinity, electrostatic potential, etc. Output is sent to standard output using the Gaussian Cube format.

Options

If no filename is given, obprobe will give all options including the example probes.

-s stepsize

Set the resolution of the grid (stepsize)

-p padding

Set the padding — extra distance on each side of the box formed by the molecule.

type

MMFF94 atom type

pchg

MMFF94 partial charge

Examples

Probe the file pyridines.sdf using a carbonyl oxygen — a hydrogen bond acceptor with partial charge -0.57:

obprobe 7 -0.57 pyridines.sdf

Probe the file pyridines.sdf using a phenyl carbon atom — a hydrophobic atom with no partial charge:

obprobe 37 0.0 pyridines.sdf