[gmx-users] Error in pdb2gmx

Justin Lemkul jalemkul at vt.edu
Tue Apr 30 12:03:11 CEST 2013

On 4/30/13 2:59 AM, Nikunj Maheshwari wrote:
> Dear all,
> I got an error while using pdb2gmx command (pdb2gmx -f 123.pdb -o
> output.gro)
> I used 13. GROMOS 53a6 force field
> "Fatal error:
> Atom HA in residue GLU 1 was not found in rtp entry GLU with 12 atoms while
> sorting atoms.
> For a hydrogen, this can be a different protonation state, or it
> might have had a different number in the PDB file and was rebuilt
> (it might for instance have been H3, and we only expected H1 & H2).
> Note that hydrogens might have been added to the entry for the N-terminus.
> Remove this hydrogen or choose a different protonation state to solve it.
> Option -ignh will ignore all hydrogens in the input."
> So I used -glu option in pdb2gmx (pdb2gmx -f 123.pdb -o output.gro -glu)
> I get the following options.
> Which GLUTAMIC ACID type do you want for residue 1
> 0. Not protonated (charge -1) (GLU)
> 1. Protonated (charge 0) (GLUH)
> Both options give the same error as before.
> The same error occurs for HB1 as well.
> Will I have to edit the pdb or rtp file? Or any other suggestions?

Read the error message again; it tells you what to do.

Consider what you're doing - you're supplying a united-atom force field with an 
all-atom structure.  The chosen parameter set doesn't have explicit hydrogens on 
nonpolar groups.  Hence pdb2gmx complains that you're giving it atoms it doesn't 
understand.  Use of -ignh solves this issue, which is precisely what the error 
message is telling you.



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


More information about the gromacs.org_gmx-users mailing list