"obprobe" - Create Electrostatic Probe Grid

Q

What Is "obprobe" command? How to use it to optimize the geometry and minimize the energy for a given molecule?

✍: FYIcenter.com

A

"obprobe" command is a command line tool provided in the Open Babel package that allows you to Create Electrostatic Probe Grid for a given molecule.

Here is the user manual of the "obprobe" command.

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

Here is an exampes of Create Electrostatic Probe Grid for the tyrosine molecule:

1. Run the "obprobe" command to generate the electrostatic probe grid.

fyicenter$ obprobe 7 -0.57 toluene.sdf 
OBForceFieldMMFF94::GetGrid(0.5, 7)
xDim = 25, yDim = 29, zDim = 21
15225/15225

2. Look at the electrostatic probe grid file:

fyicenter$ head -30 tyrosine_7_-0.570000.cube 
*****

  -13  -14.358327  -12.283219   -9.448630
   33    0.944863    0.000000    0.000000
   27    0.000000    0.944863    0.000000
   21    0.000000    0.000000    0.944863
    6    6.000000   -1.636503   -0.944863    0.000000
    6    6.000000   -3.273194   -0.000000    0.000000
    6    6.000000   -3.273194    1.889726    0.000000
    6    6.000000   -1.636503    2.834589    0.000000
    6    6.000000   -0.000000    1.889726    0.000000
    6    6.000000    0.000000    0.000000    0.000000
    6    6.000000    1.636503   -0.944863    0.000000
    6    6.000000    3.273194    0.000000    0.000000
    6    6.000000    4.909697   -0.944863    0.000000
    8    8.000000    4.909697   -2.834589    0.000000
    8    8.000000    6.546200    0.000000    0.000000
    7    7.000000    3.273194    1.889726    0.000000
    8    8.000000   -4.909697    2.834589    0.000000
     1   1
  6.19343E+02  6.19923E+02  6.20471E+02  6.20980E+02  6.21441E+02  6.21847E+02
  6.22191E+02  6.22466E+02  6.22667E+02  6.22789E+02  6.22830E+02  6.22789E+02
  6.22667E+02  6.22466E+02  6.22191E+02  6.21847E+02  6.21441E+02  6.20980E+02
  6.20471E+02  6.19923E+02  6.19343E+02  6.20188E+02  6.20820E+02  6.21420E+02
  6.21978E+02  6.22485E+02  6.22934E+02  6.23315E+02  6.23621E+02  6.23845E+02
  6.23981E+02  6.24027E+02  6.23981E+02  6.23845E+02  6.23621E+02  6.23315E+02
  6.22934E+02  6.22485E+02  6.21978E+02  6.21420E+02  6.20820E+02  6.20188E+02
  6.21044E+02  6.21733E+02  6.22388E+02  6.23001E+02  6.23561E+02  6.24058E+02
  6.24481E+02  6.24821E+02  6.25070E+02  6.25222E+02  6.25273E+02  6.25222E+02
  6.25070E+02  6.24821E+02  6.24481E+02  6.24058E+02  6.23561E+02  6.23001E+02

fyicenter$ tail tyrosine_7_-0.570000.cube 
  6.26071E+02  6.26480E+02  6.26782E+02  6.26967E+02  6.27029E+02  6.26967E+02
  6.26782E+02  6.26480E+02  6.26071E+02  6.25567E+02  6.24980E+02  6.24325E+02
  6.23615E+02  6.22864E+02  6.22083E+02  6.21224E+02  6.21941E+02  6.22626E+02
  6.23271E+02  6.23862E+02  6.24390E+02  6.24842E+02  6.25206E+02  6.25474E+02
  6.25639E+02  6.25694E+02  6.25639E+02  6.25474E+02  6.25206E+02  6.24842E+02
  6.24390E+02  6.23862E+02  6.23271E+02  6.22626E+02  6.21941E+02  6.21224E+02
  6.20369E+02  6.21025E+02  6.21651E+02  6.22236E+02  6.22771E+02  6.23245E+02
  6.23650E+02  6.23976E+02  6.24215E+02  6.24361E+02  6.24410E+02  6.24361E+02
  6.24215E+02  6.23976E+02  6.23650E+02  6.23245E+02  6.22771E+02  6.22236E+02

To view the electrostatic probe grid in the above file, you drag drop the file to the OpenMX viewer.

 

"obrotamer" - Generate Random Rotational Isomers

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Other Open Babel Commands

⇑⇑ Open Babel Tutorials

2020-10-26, 231👍, 0💬