"obrotamer" - Generate Random Rotational Isomers
What Is "obrotamer" command? How to use it to Generate Random Rotational Isomers for a given molecule?
"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 rotational isomers against the original molecule structure, which is the first one in the first row:
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Molecule Summary: ID: FYI-1000049 SMILES: Received at FYIcenter.com on: 2020-05-18