"obrotamer" - Generate Random Rotational Isomers

Q

What Is "obrotamer" command? How to use it to Generate Random Rotational Isomers for a given molecule?

✍: FYIcenter.com

A

"obrotamer" command is a command line tool provided in the Open Babel package that allows you to Generate Random Rotational Isomers for a given molecule.

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

NAME
     obrotamer -- generate conformer/rotamer coordinates

SYNOPSIS
     obrotamer filename

DESCRIPTION
     The obrotamer tool can be used as part of a conformational search by generating 
     random isomers based on rotating dihedral angles. These rotamers are not 
     conformers -- that is, obrotamer does not perform geometry optimization
     after generating the rotamer structure. The obminimize tool can do geometry 
     optimization using molecular mechanics.

EXAMPLES
           obrotamer baseconformer.sdf >rotamer1.sdf

     Generate a random rotational isomer of baseconformer.sdf and write it to rotamer1.sdf

Here is an example of generating random Rotational Isomers with the "obminimize" command:

1. Create a sample molecule with some rotatable bonds:

fyicenter$ obabel "-:CC(N)CCC(C)O" -O sample.sdf --gen2D 
1 molecule converted

2. Generate 3 random rotational isomers from the sample molecule:

fyicenter$ obrotamer sample.sdf > sample-isomer-1.sdf 
 Number of rotatable bonds: 3
 
fyicenter$ obrotamer sample.sdf > sample-isomer-2.sdf 
 Number of rotatable bonds: 3
 
fyicenter$ obrotamer sample.sdf > sample-isomer-3.sdf 
 Number of rotatable bonds: 3 

3. Put the sample molecule and it isomers together in a single SVG picture:

fyicenter$ babel sample.sdf sample-*.sdf sample-isomers.svg -xcols2 
4 molecules converted
104 audit log messages 

4. Compare rotatiobal isomers against the original molecule structure, which is the first one in the first row:

Sample Molecule and Its Rotational Isomers
Sample Molecule and Its Rotational Isomers

 

"obrotate" - Rotate Dihedral Angles with SMARTS

"obprobe" - Create Electrostatic Probe Grid

Other Open Babel Commands

⇑⇑ Open Babel Tutorials

2020-10-26, 179👍, 0💬