[gmx-users] PDB2GMX Fatal Error

Justin Lemkul jalemkul at vt.edu
Wed Mar 1 12:15:06 CET 2017

On 3/1/17 3:23 AM, Syed Azeem wrote:
>> Use -ignh in pdb2gmx.
> Hi Reza,
> I tried -ignh, it's working fine.
> But i need to calculate H-bonds after docking the same peptide. Then
> the same error will crop up and I won't be able to calculate H-bonds.

The use of -ignh has nothing to do with whether or not you can calculate 
hydrogen bonds.

The more complete explanation about -ignh is that H atoms in the input 
coordinates are ignored, then rebuilt according to the force field's .hdb file. 
Your problem was that your H atom nomenclature was non-standard, or at least did 
not conform to the force field's expectations, so you got a fatal error.  You 
can easily confirm in the topology and coordinates produced when using -ignh 
that in fact all of the H you need are there.  pdb2gmx just rebuilt them so you 
didn't have to waste time renaming all your non-conforming H atoms.


>>> 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


Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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