How to Remove Water Molecules from a PDB File (3 Free Ways)

By BioDockify Computational Research Team · September 3, 2026 · Tutorials

Remove water from a PDB file three free ways: grep one-liner, Open Babel, and a text editor, plus which HETATM records to keep, conserved waters, and a verification checklist.

Read the complete article with tables, code and references on BioDockify.

Key References

• Berman HM et al. The Protein Data Bank. Nucleic Acids Res. 2000;28:235-242. doi:10.1093/nar/28.1.235
• O\u2019Boyle NM et al. Open Babel: an open chemical toolbox. J Cheminform. 2011;3:33. doi:10.1186/1758-2946-3-33
• wwPDB format documentation and RCSB download tools, wwpdb.org.

Scope & Limitations

Examples strip all waters; conserved or catalytic waters require selective retention as described in the text