[gmx-users] Missing H from residue

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 9 22:26:12 CET 2009

Jack Shultz wrote:
> 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?

Yep - you may need a well-formatted .hdb file, like the message says :-) 
You should check out whether the AMBER port you installed supports this 
feature or not. Alternatively, have a look in the file and with a viewer 
to see what is present for residue 1 and how the atoms are named, and 
whether renaming some atoms will fix the issue.


> 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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