This is the command obprobe that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
PROGRAM:
NAME
obprobe — create electrostatic probe grid
SYNOPSIS
obprobe [OPTIONS] type pchg filename
DESCRIPTION
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
Use obprobe online using onworks.net services
