Hi Tim, On 2/6/14, 10:52 AM, Tim Gruene wrote: > the simple and qucik command > > egrep -v "^ATOM|HETATM.*H$" your.pdb > your_noH.pdb > > should also work. just out of curiosity I did (copy-paste of your example) egrep -v "^ATOM|HETATM.*H$\" m.pdb > m_noH.pdb and I got: Illegal variable name. Pavel