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How to minimize the energy of a molecule using OpenBabel

📅 2013-May-12 ⬩ ✍️ Ashwin Nanjappa ⬩ 📚 Archive

The obminimize program that ships with Open Babel can be used to minimize the energy of a molecule and write the minimized molecule to a file.

To minimize the energy of a molecule named foo.sdf:

$ obminimize foo.sdf

To minimize the energy and write the minimized molecule to a file:

$ obminimize -o sdf foo.sdf > out.sdf

Use the -o parameter to specify the output file format and redirect the output to write the output file.

Tried with: Open Babel 2.3.0 and Ubuntu 12.04 LTS