[gmx-users] PDB2GMX Fatal Error

Syed Azeem syedazeemullah186 at gmail.com
Wed Mar 1 09:23:06 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.

>> 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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