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

Shima Arasteh shima_arasteh2001 at yahoo.com
Mon May 14 17:19:44 CEST 2012

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? 

-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?

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