[gmx-users] PDB2GMX Fatal Error

Reza Esmaeili goldeagle.93 at gmail.com
Wed Mar 1 07:54:49 CET 2017

Use -ignh in pdb2gmx.

> On Mar 1, 2017, at 10:22, Syed Azeem <syedazeemullah186 at gmail.com> wrote:
> Hi all,
> I tried passing a predicted peptide (16-mer) into GMX and ended up
> with a fatal error regarding hydrogen. I tried ignoring the hydrogens
> using -ignh command. But I'll need to calculate H-bonds for the next
> analysis, as I'll dock this peptide into a target protein.
> Fatal error:
> Atom HB3 in residue ASN 1 was not found in rtp entry NASN with 16 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.
> How to solve this issue?
> Thanks in advance
> Azeem
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