[gmx-users] atom H is missing in the first residue in a chain

Justin A. Lemkul jalemkul at vt.edu
Wed Jan 14 19:59:00 CET 2009

Zhong Zheng wrote:
> Hi all
> I am running Gromacs on a three-chain protein. The program complains 
> about "atom H is missing in residue ALA 1 in the pdb file, You might 
> need to add atom H to the hydrogen database of residue ALA in the file 
> ff???.hdb (see the manual)". It's a warning message. I can use the 
> option -missing to ignore it. However I would like to understand this. 
> It's always the first residue in the chain. So I am thinking this is 
> because they are the n-terminus. Then why no complain about c-terminus? 
> How can I fix this?

Use -ignh to allow the relevant .hdb file to add the appropriate hydrogens.  The 
problem is that, without -ignh, pdb2gmx expects all atoms (including H) to be 
present in the .pdb file.  If you are using a crystal structure, this 
requirement will not be satisfied.

Likely pdb2gmx does not complain about the C-terminus because it is 
unprotonated, or otherwise the program exits after finding a missing N-terminal 

As an aside, using -missing is generally a very bad idea, unless you have a very 
specific (and anticipated!) reason to use it.


> Thanks a lot.
> Zhong Zheng
> Ph.D candidate
> Physics Dept., City College-CUNY
> Marshak Science Building J-419 , 
> 160 Convent Ave, 
> New York, NY 10031 USA
> Tel: (212)650-6079 
> MCCE wiki: scratchpad.wikia.com/wiki/MCCE 
> <http://scratchpad.wikia.com/wiki/MCCE>
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Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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