[gmx-users] fatal error: missing H atom in .pdb file

Justin A. Lemkul jalemkul at vt.edu
Mon May 14 18:12:42 CEST 2012

On 5/14/12 11:19 AM, Shima Arasteh wrote:
> Dear gmx users,
> I changed the aminoacids.rtp file recently.
> Now, when I run pdb2gmx, I get the fatal error:
> atom H is missing in residue For 0 in the pdb file
> You might need to add atom H to the hydrogen database of building block For
> in the file aminoacids.hdb
> -Is it may as a result of some problems in .rtp file?

The error states that an H atom is specified in the .rtp entry but is not 
present in the .pdb file.  They two must match.  In the case of H atoms, they 
can be rebuilt if a suitable .hdb entry exists.  See the manual.

> -May I use -missing option and get a appropriate output? As I see in manual, I
> can use this option when I want to generate specialized topologies for amino
> acid-like molecules to take advantage of .rtp entries. The part which I entered
> in .rtp file is a formyl as the N-terminal for the protein. I guess I can use
> -missing option, Can't I?

There are very limited cases where the -missing option should be used.  This is 
not one of them.



Justin A. Lemkul, Ph.D.
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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