[gmx-users] Missing H from residue

Justin A. Lemkul jalemkul at vt.edu
Mon Nov 9 23:38:51 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?
> 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)

When using AMBER, the first residue should be NGLU, not just GLU.  Likewise for 
the C-terminus (CXXX).  If you name the residue appropriately, the right 
hydrogens should be added based on the .hdb entry.


> -------------------------------------------------------
> 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
> -------------------------------------------------------


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


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