[gmx-users] PDB2GMX Fatal Error

Syed Azeem syedazeemullah186 at gmail.com
Wed Mar 1 13:45:52 CET 2017

>>> 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.
> -Justin
Now I understood the -ignh option.
Thanks for the explanation

>>>> 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
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> 20 Penn St.
> Baltimore, MD 21201
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> ==================================================

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