[gmx-users] Missing H from residue

Jack Shultz js at drugdiscoveryathome.com
Mon Nov 9 22:22:10 CET 2009

I tried to protonate my pdb file using openbabel
babel -ipdb fzd8min_renum_SS.pdb -opdb Protein.pdb -h

Then I ran pdb2gmx with the following

pdb2gmx -ff amber99sb -f ProteinAmber.pdb -o Protein2.pdb -p
Protein.top -water spce -ignh

But apparently I am missing a H from my first residue. Is there an
easy way to add missing atoms?

WARNING: atom H is missing in residue GLU 1 in the pdb file
         You might need to add atom H to the hydrogen database of residue GLU
         in the file ff???.hdb (see the manual)

Program pdb2gmx, VERSION 4.0.5
Source code file: pdb2top.c, line: 704

Fatal error:
There were 1 missing atoms in molecule Protein, if you want to use
this incomplete topology anyhow, use the option -missing



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