[gmx-users] How to handle incomplete PDB file?

Lee Soin nomadoro at gmail.com
Tue Mar 3 13:46:15 CET 2009

While processing a PDB file, pdb2gmx ended up with the warning

WARNING: atom CG not found in residue 14 while adding atom

and the error

Fatal error:
Atom CG not found in residue ASP14 while adding hydrogens

Specifying -missing in pdb2gmx doesn't work.

In the original PDB file, a few missing atoms are listed.

What to do in this situation?

Sun Li
Department of Physics
Nanjing University, China
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