[gmx-users] PDB2GMX Fatal Error

Syed Azeem syedazeemullah186 at gmail.com
Wed Mar 1 07:52:36 CET 2017

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


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