What should I do if something appears like this?

GROMACS version:
GROMACS modification: Yes/No
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Fatal error:

Atom HD1 in residue HIS 114 was not found in rtp entry HISE with 17 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.

For more information and tips for troubleshooting, please check the GROMACS

website at Errors - Gromacs


I guess you get this error in the pre-processing using gmx pdb2gmx. To solve the issue you can run gmx pdb2gmx with the option -ignh and leave the tool assigns the tautomeric state of HIS according to its criteria. In case you want a specific tautomeric state you can use the option -his that allow to assign manually the state for each his in the system.